debian/0000775000000000000000000000000012253224244007170 5ustar debian/rules0000775000000000000000000002460212251423376010261 0ustar #!/usr/bin/make -f # # build script for GROMACS # export DH_VERBOSE=1 PACKAGE := gromacs # OpenMPI is only supported on a subset of architectures at this time. # This list should remain synced with the Build-Depends and the Architecture # line of gromacs-openmpi in debian/control. OPENMPI_ARCH = alpha amd64 armel armhf i386 ia64 powerpc powerpcspe ppc64 sparc sparc64 kfreebsd-i386 kfreebsd-amd64 hurd-i386 DEB_HOST_ARCH ?= $(shell dpkg-architecture -qDEB_HOST_ARCH) # add hardening flags, using hardening-wrapper export DEB_BUILD_HARDENING=1 CFLAGS = ifneq (,$(findstring debug,$(DEB_BUILD_OPTIONS))) CFLAGS += -g -Wall endif ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) CFLAGS += -O0 endif LDFLAGS += -Wl,--as-needed COMMON_CONFIG_PARAMS = \ $(CURDIR) \ -DCMAKE_VERBOSE_MAKEFILE=ON \ -DCMAKE_INSTALL_PREFIX="/usr" \ -DCMAKE_EXE_LINKER_FLAGS="$(LDFLAGS)" \ -DCMAKE_SKIP_RPATH=TRUE \ -DGMX_X11=ON ifneq ($(CFLAGS),) COMMON_CONFIG_PARAMS += -DCMAKE_C_FLAGS="$(CFLAGS)" endif # Force compiler to use no more than SSE2 CPU optimizations, for broadest # compatibility. For local compilations, pass DEB_BUILD_OPTIONS=cpuopt # for automatic detection of the best available option. Planned for an # overhaul in GROMACS 5.0 with proper runtime detection. kfreebsd-* doesn't # yet support the higher extensions anyhow, no special casing needed. ifneq (,$(findstring cpuopt,$(DEB_BUILD_OPTIONS))) ifneq (,$(findstring $(DEB_HOST_ARCH),i386 amd64)) COMMON_CONFIG_PARAMS += -DGMX_CPU_ACCELERATION=SSE2 endif endif # Include "gpu" in DEB_BUILD_OPTIONS to build GPU-accelerated binaries as well. # See INSTALL-GPU. This build option is not tested, please send comments. # You must have OpenMM development headers (not packaged) and "nvidia-cuda-dev" # installed! ifneq (,$(findstring gpu,$(DEB_BUILD_OPTIONS))) COMMON_CONFIG_PARAMS += -DGMX_OPENMM=ON endif MPICH_CONFIG_PARAMS = \ -DGMX_MPI=ON \ -DGMX_X11=OFF \ -DGMX_DEFAULT_SUFFIX=FALSE OPENMPI_CONFIG_PARAMS = \ -DGMX_MPI=ON \ -DGMX_DEFAULT_SUFFIX=FALSE \ -DGMX_X11=OFF \ -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib $(LDFLAGS)" # optional parallel build ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS))) MAKE += -j$(NUMJOBS) endif configure: configure-stamp configure-stamp: dh_testdir (mkdir -p build/basic; cd build/basic; cmake $(COMMON_CONFIG_PARAMS) -DGMX_MPI=OFF) (mkdir -p build/basic-dp; cd build/basic-dp; cmake $(COMMON_CONFIG_PARAMS) -DGMX_MPI=OFF -DGMX_DOUBLE=ON) (mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich cmake \ $(COMMON_CONFIG_PARAMS) $(MPICH_CONFIG_PARAMS) -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich") (mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich cmake \ $(COMMON_CONFIG_PARAMS) $(MPICH_CONFIG_PARAMS) -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich") ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH))) (mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi cmake \ $(COMMON_CONFIG_PARAMS) $(OPENMPI_CONFIG_PARAMS) -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi") (mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi cmake \ $(COMMON_CONFIG_PARAMS) $(OPENMPI_CONFIG_PARAMS) -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi") endif touch $@ build: configure-stamp build-basic build-mpich build-openmpi build-arch: build build-indep: build build-basic: configure-stamp dh_testdir $(MAKE) -C build/basic $(MAKE) -C build/basic-dp touch $@ build-mpich: configure-stamp dh_testdir $(MAKE) -C build/mpich mdrun $(MAKE) -C build/mpich-dp mdrun sed -e 's/#MPIABBR#/mpich/g' -e 's/#MPIPROG#/MPICH2/g' \ < debian/gromacs-parallel.README.Debian.in \ > debian/gromacs-mpich.README.Debian touch $@ build-openmpi: configure-stamp dh_testdir ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH))) $(MAKE) -C build/openmpi mdrun $(MAKE) -C build/openmpi-dp mdrun sed -e 's/#MPIABBR#/openmpi/g' -e 's/#MPIPROG#/OpenMPI/g' \ < debian/gromacs-parallel.README.Debian.in \ > debian/gromacs-openmpi.README.Debian endif touch $@ clean: dh_testdir dh_testroot rm -rf build dh_clean build-basic build-mpich build-openmpi configure-stamp \ debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian install: build install-basic install-mpich install-openmpi dh_testdir dh_testroot dh_prep -pgromacs-data -pgromacs-dev dh_installdirs -pgromacs-data mv $(CURDIR)/debian/gromacs/usr/share/gromacs/top \ $(CURDIR)/debian/gromacs-data/usr/share/gromacs mv $(CURDIR)/debian/gromacs/usr/share/gromacs/html \ $(CURDIR)/debian/gromacs-data/usr/share/doc/gromacs mv $(CURDIR)/debian/gromacs/usr/share/man \ $(CURDIR)/debian/gromacs-data/usr/share/man # some of the default installation directories for documentation and # example shell scripts are not FHS-friendly; move them appropriately mv $(CURDIR)/debian/gromacs/usr/bin/GMXRC* \ $(CURDIR)/debian/gromacs/usr/bin/completion* \ $(CURDIR)/debian/gromacs-data/usr/share/gromacs/shell-specific chmod 644 $(CURDIR)/debian/gromacs-data/usr/share/gromacs/shell-specific/* dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/gromacs-data/html dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/gromacs-dev/html # this name is also give in documentation dh_link -pgromacs-data usr/share/doc/gromacs-data/copyright usr/share/doc/gromacs-data/COPYING # one lintian warning is overridden: # - script-not-executable: demo scripts outside of $PATH dh_lintian -pgromacs-data # rename a pair of Perl scripts to drop the .pl extension (Policy 10.4) mv $(CURDIR)/debian/gromacs/usr/bin/demux.pl $(CURDIR)/debian/gromacs/usr/bin/demux mv $(CURDIR)/debian/gromacs/usr/bin/xplor2gmx.pl $(CURDIR)/debian/gromacs/usr/bin/xplor2gmx dh_installdirs -pgromacs-dev mv $(CURDIR)/debian/gromacs/usr/include $(CURDIR)/debian/gromacs-dev/usr/include # catch normal libraries plus all applicable MPI variants mv $(CURDIR)/debian/gromacs/usr/lib/*.so $(CURDIR)/debian/gromacs/usr/lib/pkgconfig $(CURDIR)/debian/gromacs-dev/usr/lib # arguably these should be in -openmpi-dev packages or the like; they'd be so tiny that # it's barely worth the effort, and keeping library symlinks in the -openmpi/-mpich # packages helps avoid a potential policy violation; disabling these moves # mv $(CURDIR)/debian/gromacs-mpich/usr/lib/*.so $(CURDIR)/debian/gromacs-dev/usr/lib #ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH))) # mv $(CURDIR)/debian/gromacs-openmpi/usr/lib/*.so $(CURDIR)/debian/gromacs-dev/usr/lib #endif mv $(CURDIR)/debian/gromacs/usr/share/gromacs/template $(CURDIR)/debian/gromacs-dev/usr/share/gromacs/template # remaining documentation catch-all mv $(CURDIR)/debian/gromacs/usr/share/gromacs/* $(CURDIR)/debian/gromacs-data/usr/share/doc/gromacs -rmdir $(CURDIR)/debian/gromacs/usr/share/gromacs install-basic: build dh_testdir dh_testroot dh_prep -pgromacs dh_installdirs -pgromacs $(MAKE) -C build/basic install DESTDIR=$(CURDIR)/debian/gromacs $(MAKE) -C build/basic-dp install DESTDIR=$(CURDIR)/debian/gromacs rm -f $(CURDIR)/debian/gromacs/usr/share/man/man1/*_d.1 dh_installman -pgromacs debian/man/g_*.1 for manpage in $(CURDIR)/debian/gromacs/usr/share/man/man1/*.1; do \ dh_link -pgromacs usr/share/man/man1/`basename $${manpage}` usr/share/man/man1/`basename $${manpage} .1`_d.1 ; \ done # man pages for a pair of Perl scripts are installed *after* the _d duplication, # as they have no double-precision variants. dh_installman -pgromacs debian/man/demux.1 debian/man/xplor2gmx.1 # this program is currently broken - keep it from shipping until fixed rm $(CURDIR)/debian/gromacs/usr/bin/g_pme_error $(CURDIR)/debian/gromacs/usr/bin/g_pme_error_d # two lintian warnings are overridden: # - package-name-doesnt-match-sonames: the libraries are private to # GROMACS, and it's unlikely that any new package will start using # them; therefore, separate lib packages would just be bloat. # This is also overridden for the -mpich and -openmpi packages. # - shlib-with-executable-stack: it's a side effect of the ASM inner # loops (i386/amd64 only) dh_lintian -pgromacs install-mpich: build dh_testdir dh_testroot dh_prep -pgromacs-mpich dh_installdirs -pgromacs-mpich $(MAKE) -C build/mpich install-mdrun DESTDIR=$(CURDIR)/debian/gromacs-mpich $(MAKE) -C build/mpich-dp install-mdrun DESTDIR=$(CURDIR)/debian/gromacs-mpich # temporary workaround for RPATH issue in mpich3 chrpath -d $(CURDIR)/debian/gromacs-mpich/usr/bin/* $(CURDIR)/debian/gromacs-mpich/usr/lib/* dh_installman -pgromacs-mpich debian/man/mdrun_mpi.mpich.1 dh_link -pgromacs-mpich usr/share/man/man1/mdrun_mpi.mpich.1.gz usr/share/man/man1/mdrun_mpi_d.mpich.1.gz dh_lintian -pgromacs-mpich install-openmpi: build dh_testdir dh_testroot dh_prep -pgromacs-openmpi ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH))) dh_installdirs -pgromacs-openmpi $(MAKE) -C build/openmpi install-mdrun DESTDIR=$(CURDIR)/debian/gromacs-openmpi $(MAKE) -C build/openmpi-dp install-mdrun DESTDIR=$(CURDIR)/debian/gromacs-openmpi dh_installman -pgromacs-openmpi debian/man/mdrun_mpi.openmpi.1 dh_link -pgromacs-openmpi usr/share/man/man1/mdrun_mpi.openmpi.1.gz usr/share/man/man1/mdrun_mpi_d.openmpi.1.gz dh_lintian -pgromacs-openmpi endif binary-indep: build install dh_testdir dh_testroot dh_installchangelogs -i dh_installdocs -pgromacs-data dh_compress -i dh_fixperms -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i binary-arch: build install dh_testdir -s dh_testroot -s dh_installchangelogs -s dh_installdocs -s dh_strip -A dh_link -s dh_compress -s dh_fixperms -s dh_makeshlibs -s dh_shlibdeps -pgromacs -L gromacs -l debian/gromacs/usr/lib dh_shlibdeps -pgromacs-mpich -L gromacs-mpich -l debian/gromacs-mpich/usr/lib ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH))) dh_shlibdeps -pgromacs-openmpi -L gromacs-openmpi -l debian/gromacs-openmpi/usr/lib endif dh_gencontrol -s dh_installdeb -s dh_md5sums -s dh_builddeb -s binary: binary-indep binary-arch .PHONY: binary binary-arch binary-indep build clean install install-basic install-mpich install-openmpi # Because multiple versions of the same programs are created using the same source tree, # the various build-* targets can't be compiled simultaneously. # Passing down -j# to child make processes remains unaffected. .NOTPARALLEL: debian/watch0000664000000000000000000000024212221637146010223 0ustar # See uscan(1) for format version=3 opts=pasv,uversionmangle=s/[-_]((pre|beta)[^.]+)/~$1/ \ ftp://ftp.gromacs.org/pub/gromacs/gromacs-([\d\.betapr_-]*)\.tar\.gz debian/gromacs-openmpi.lintian-overrides0000664000000000000000000000134312201767060015652 0ustar gromacs-openmpi: package-name-doesnt-match-sonames # Adaptive Resolution Molecular Dynamics Simulation gromacs-openmpi: spelling-error-in-binary usr/lib/libgmxpreprocess_mpi.openmpi.so.8 AdResS Address gromacs-openmpi: spelling-error-in-binary usr/lib/libgmxpreprocess_mpi_d.openmpi.so.8 AdResS Address gromacs-openmpi: spelling-error-in-binary usr/lib/libmd_mpi.openmpi.so.8 AdResS Address gromacs-openmpi: spelling-error-in-binary usr/lib/libmd_mpi_d.openmpi.so.8 AdResS Address gromacs-openmpi: spelling-error-in-binary usr/lib/libgmx_mpi.openmpi.so.8 AdResS Address gromacs-openmpi: spelling-error-in-binary usr/lib/libgmx_mpi_d.openmpi.so.8 AdResS Address # too small to merit a -dev package of its own non-dev-pkg-with-shlib-symlink debian/gromacs.README.Debian0000664000000000000000000000710712241471134012667 0ustar GROMACS for Debian ------------------ The basic 'gromacs' package contains only single-threaded binaries. For multiple threads or machines, you will need the MPI-enabled version of mdrun. Depending on your MPI implementation of choice, install either the 'gromacs-openmpi' or 'gromacs-mpich'. If you are setting up an MPI installation for the first time and have no existing preference, then 'gromacs-openmpi' is your best choice. OpenMPI is currently the most active MPI development project, and has incorporated several other MPI implementations under its umbrella. Also consider installing the 'openmpi-doc' package for additional documentation. OpenMPI has superseded the LAM-MPI project. 'gromacs-mpich' supports the MPICH3 implementation. Although less commonly used in the GROMACS community than OpenMPI (and its predecessor LAM), it does support more architectures and also has an active developer base. Both of the MPI packages install their version of 'mdrun' as 'mdrun_mpi', so you can keep both regular and MPI binaries on the same machine. See the README files in /usr/share/doc/gromacs-openmpi or /usr/share/doc/gromacs-mpich (when installed) for additional information. Finally, the MPI packages can be installed independently of the main gromacs package, and unlike the main package, do not require the X Window System to be installed. This makes them suitable for installation on a large cluster, where you only intend to do serious number-crunching on that node and perform all interactive tasks on another machine. Additional Documentation ------------------------ In addition to the documentation included in this package, the GROMACS website contains several additional manuals, tutorials, and checklists of use to all skill levels, at . demux.pl and xplor2gmx.pl ------------------------- You may see references to these scripts on the GROMACS mailing lists. In this package, they have been renamed without their suffixes: demux and xplor2gmx. Double Precision Binaries ------------------------- The standard version of all binaries have been compiled for single- precision floating point operations. For some applications, this may result in unacceptably large numeric instabilities. Double-precision calculations can often solve such problems, with a tradeoff in speed (typically a ~30% slowdown on i386). Binaries compiled for DP have a "_d" suffix, and in all other ways operate identically to their single- precision counterparts. CPU Optimizations ----------------- On amd64 and i386 architectures, the compiler is restricted to SSE2 extensions. Some systems may have additional SIMD extensions available that can speed execution by large amounts, but are not available on all CPUs of that architecture (e.g. AVX extensions on amd64 that are only present on Intel's Sandy Bridge or AMD Bulldozer and subsequent chips). To compile a package with autodetection of available extensions, use the environment variable DEB_BUILD_OPTIONS=cpuopt . This choice of default should work on all amd64 CPUs, and i386 CPUs from the Intel Pentium 4 or AMD Opteron/Athlon 64 and forward (roughly speaking, all new systems since 2001). Although this does exclude certain very old i386 systems, the performance tradeoffs from disabling SSE2 are severe; you may not get much performance-per-watt on such CPUs. On such CPUs, compiling your own binaries is mandatory. For more information about GROMACS and CPU acceleration, please see . -- Nicholas Breen , Fri, 15 Nov 2013 11:12:19 -0800 debian/man/0000775000000000000000000000000012065651554007754 5ustar debian/man/g_dos.10000664000000000000000000000710711636465015011134 0ustar .TH g_dos 1 "Wed 21 Sep 2011" "" "GROMACS suite, VERSION 4.5.5" .SH NAME g_dos \- compute density of states from a simulation trajectory .B VERSION 4.5.5 .SH SYNOPSIS \f3g_dos\fP .BI "\-f" " traj.trr " .BI "\-s" " topol.tpr " .BI "\-n" " index.ndx " .BI "\-vacf" " vacf.xvg " .BI "\-mvacf" " mvacf.xvg " .BI "\-dos" " dos.xvg " .BI "\-g" " dos.log " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .BI "\-b" " time " .BI "\-e" " time " .BI "\-dt" " time " .BI "\-[no]w" "" .BI "\-xvg" " enum " .BI "\-[no]v" "" .BI "\-[no]recip" "" .BI "\-[no]abs" "" .BI "\-[no]normdos" "" .BI "\-T" " real " .BI "\-acflen" " int " .BI "\-[no]normalize" "" .BI "\-P" " enum " .BI "\-fitfn" " enum " .BI "\-ncskip" " int " .BI "\-beginfit" " real " .BI "\-endfit" " real " .SH DESCRIPTION \&\fB g_dos\fR computes the Density of States from a simulation. \&In order for this to be meaningful the velocities must be saved \&in the trajectory with sufficiently high frequency such as to cover \&all vibrations. For flexible systems that would be around a few fs \&between saving. Properties based on the DoS are printed on the \&standard output. .SH FILES .BI "\-f" " traj.trr" .B Input Full precision trajectory: trr trj cpt .BI "\-s" " topol.tpr" .B Input Run input file: tpr tpb tpa .BI "\-n" " index.ndx" .B Input, Opt. Index file .BI "\-vacf" " vacf.xvg" .B Output xvgr/xmgr file .BI "\-mvacf" " mvacf.xvg" .B Output xvgr/xmgr file .BI "\-dos" " dos.xvg" .B Output xvgr/xmgr file .BI "\-g" " dos.log" .B Output Log file .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 19" Set the nicelevel .BI "\-b" " time" " 0 " First frame (ps) to read from trajectory .BI "\-e" " time" " 0 " Last frame (ps) to read from trajectory .BI "\-dt" " time" " 0 " Only use frame when t MOD dt = first time (ps) .BI "\-[no]w" "no " View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR .BI "\-[no]v" "yes " Be loud and noisy. .BI "\-[no]recip" "no " Use cm\-1 on X\-axis instead of 1/ps for DoS plots. .BI "\-[no]abs" "no " Use the absolute value of the Fourier transform of the VACF as the Density of States. Default is to use the real component only .BI "\-[no]normdos" "no " Normalize the DoS such that it adds up to 3N. This is a hack that should not be necessary. .BI "\-T" " real" " 298.15" Temperature in the simulation .BI "\-acflen" " int" " \-1" Length of the ACF, default is half the number of frames .BI "\-[no]normalize" "yes " Normalize ACF .BI "\-P" " enum" " 0" Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR .BI "\-fitfn" " enum" " none" Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR .BI "\-ncskip" " int" " 0" Skip N points in the output file of correlation functions .BI "\-beginfit" " real" " 0 " Time where to begin the exponential fit of the correlation function .BI "\-endfit" " real" " \-1 " Time where to end the exponential fit of the correlation function, \-1 is until the end .SH KNOWN PROBLEMS \- This program needs a lot of memory: total usage equals the number of atoms times 3 times number of frames times 4 (or 8 when run in double precision). .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>. debian/man/g_luck.10000664000000000000000000000272111542010054011263 0ustar .\" Hey, EMACS: -*- nroff -*- .\" First parameter, NAME, should be all caps .\" Second parameter, SECTION, should be 1-8, maybe w/ subsection .\" other parameters are allowed: see man(7), man(1) .TH "G_LUCK" "1" "2 Oct 2010" "GROMACS suite, Version 4.5" .\" Please adjust this date whenever revising the manpage. .\" .\" Some roff macros, for reference: .\" .nh disable hyphenation .\" .hy enable hyphenation .\" .ad l left justify .\" .ad b justify to both left and right margins .\" .nf disable filling .\" .fi enable filling .\" .br insert line break .\" .sp insert n+1 empty lines .\" for manpage-specific macros, see man(7) .SH NAME g_luck \- GROMACS installation test program .SH SYNOPSIS .B g_luck .SH DESCRIPTION .B g_luck writes a randomly selected quote to \fIstdout\fP. Normally this serves to test a freshly-compiled GROMACS installation; it also helps to maintain that air of cultural sophistication and wide-ranging appeal that characterizes any molecular dynamics package worth its force fields. .SH OPTIONS .B g_luck takes no options\. It may vary its output depending on whether the user is cool or not. .SH SEE ALSO .BR fortune (1), .BR gromacs (7) .SH AUTHOR Sadly, the current GROMACS distribution lacks official documentation for this command. This manual page was written by Nicholas Breen <\&nbreen@ofb\.net\&>, for the Debian GNU/Linux system (but may be used by others)\. debian/man/g_options.10000664000000000000000000000520711635734227012044 0ustar .TH g_options 1 "Mon 21 Mar 2011" "" "GROMACS suite, VERSION 4.5.4" .SH NAME g_options \- Utility program for generating GROMACS documentation .B VERSION 4.5.4 .SH SYNOPSIS \f3g_options\fP .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .SH DESCRIPTION \&GROMACS programs have some standard options, \&of which some are hidden by default: .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 0" Set the nicelevel .SH KNOWN PROBLEMS \- If the configuration script found Motif or Lesstif on your system, you can use the graphical interface (if not, you will get an error): \fB \-X\fR gmx_bool \fB no\fR Use dialog box GUI to edit command line options \- When compiled on an SGI\-IRIX system, all GROMACS programs have an additional option: \fB \-npri\fR int \fB 0\fR Set non blocking priority (try 128) \- Optional files are not used unless the option is set, in contrast to non\-optional files, where the default file name is used when the option is not set. \- All GROMACS programs will accept file options without a file extension or filename being specified. In such cases the default filenames will be used. With multiple input file types, such as generic structure format, the directory will be searched for files of each type with the supplied or default name. When no such file is found, or with output files the first file type will be used. \- All GROMACS programs with the exception of \fB mdrun\fR and \fB eneconv\fR check if the command line options are valid. If this is not the case, the program will be halted. \- Enumerated options (enum) should be used with one of the arguments listed in the option description, the argument may be abbreviated. The first match to the shortest argument in the list will be selected. \- Vector options can be used with 1 or 3 parameters. When only one parameter is supplied the two others are also set to this value. \- All GROMACS programs can read compressed or g\-zipped files. There might be a problem with reading compressed \fB .xtc\fR, \fB .trr\fR and \fB .trj\fR files, but these will not compress very well anyway. \- Most GROMACS programs can process a trajectory with fewer atoms than the run input or structure file, but only if the trajectory consists of the first n atoms of the run input or structure file. \- Many GROMACS programs will accept the \fB \-tu\fR option to set the time units to use in output files (e.g. for \fB xmgr\fR graphs or \fB xpm\fR matrices) and in all time options. .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>. debian/man/demux.10000664000000000000000000000314611542010054011143 0ustar .TH "demux" "1" "13 Oct 2008" "GROMACS suite, Version 4.0" .SH NAME demux \- Convert XPLOR distance restraints to Gromacs format .SH SYNOPSIS \f3demux\fP .B "md0.log " .B "extra " .SH DESCRIPTION If you would like to make your trajectories continuous again you can use .B demux to read your md0.log file (you can concatenate several if necessary) and produce a few output files. One of these is a .xvg file (\fIreplica_ndx.xvg\fR) that can be passed to .BR trjcat(1) along with the original trajectory files, in order to produce continuous trajectories. The other file (\fIreplica_temp.xvg\fR) contains the temperatures for each replica, starting at the original temperature. So if your replica of interest starts at, say, 300 K, you can follow its trajectory through temperature space. It would be interesting to add some functionality to make histograms of temperature distributions for each replica, which according to most authors, should be flat. The demuxed trajectories can be used with .BR g_kinetics(1) to obtain protein folding kinetics from REMD trajectories. .SH OPTIONS .B md0.log Log file of the trajectory run you wish to make continuous. Multiple files can be appended together. .B extra Number of times each entry in the log file will be copied. (Integer) .SH LIMITATIONS If your exchange was every N ps and you saved every M ps you can make for the missing frames by setting \fBextra\fR to (N/M - 1). If N/M is not integer, you're out of luck and you will not be able to demux your trajectories at all. .SH SEE ALSO .BR gromacs (7), .BR trjcat (1), .BR g_kinetics (1), .I debian/man/mdrun_mpi.openmpi.10000664000000000000000000004303011542010054013455 0ustar .TH mdrun_mpi 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" .SH NAME mdrun_mpi - performs a simulation, do a normal mode analysis or an energy minimization across multiple CPUs or systems .B VERSION 4.5 .SH SYNOPSIS \f3mdrun_mpi\fP .BI "\-s" " topol.tpr " .BI "\-o" " traj.trr " .BI "\-x" " traj.xtc " .BI "\-cpi" " state.cpt " .BI "\-cpo" " state.cpt " .BI "\-c" " confout.gro " .BI "\-e" " ener.edr " .BI "\-g" " md.log " .BI "\-dhdl" " dhdl.xvg " .BI "\-field" " field.xvg " .BI "\-table" " table.xvg " .BI "\-tablep" " tablep.xvg " .BI "\-tableb" " table.xvg " .BI "\-rerun" " rerun.xtc " .BI "\-tpi" " tpi.xvg " .BI "\-tpid" " tpidist.xvg " .BI "\-ei" " sam.edi " .BI "\-eo" " sam.edo " .BI "\-j" " wham.gct " .BI "\-jo" " bam.gct " .BI "\-ffout" " gct.xvg " .BI "\-devout" " deviatie.xvg " .BI "\-runav" " runaver.xvg " .BI "\-px" " pullx.xvg " .BI "\-pf" " pullf.xvg " .BI "\-mtx" " nm.mtx " .BI "\-dn" " dipole.ndx " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .BI "\-deffnm" " string " .BI "\-xvg" " enum " .BI "\-[no]pd" "" .BI "\-dd" " vector " .BI "\-nt" " int " .BI "\-npme" " int " .BI "\-ddorder" " enum " .BI "\-[no]ddcheck" "" .BI "\-rdd" " real " .BI "\-rcon" " real " .BI "\-dlb" " enum " .BI "\-dds" " real " .BI "\-gcom" " int " .BI "\-[no]v" "" .BI "\-[no]compact" "" .BI "\-[no]seppot" "" .BI "\-pforce" " real " .BI "\-[no]reprod" "" .BI "\-cpt" " real " .BI "\-[no]cpnum" "" .BI "\-[no]append" "" .BI "\-maxh" " real " .BI "\-multi" " int " .BI "\-replex" " int " .BI "\-reseed" " int " .BI "\-[no]ionize" "" .SH DESCRIPTION \&The mdrun program is the main computational chemistry engine \&within GROMACS. Obviously, it performs Molecular Dynamics simulations, \&but it can also perform Stochastic Dynamics, Energy Minimization, \&test particle insertion or (re)calculation of energies. \&Normal mode analysis is another option. In this case mdrun \&builds a Hessian matrix from single conformation. \&For usual Normal Modes\-like calculations, make sure that \&the structure provided is properly energy\-minimized. \&The generated matrix can be diagonalized by g_nmeig. \fIThis version of the program will only run while using the OpenMPI parallel computing library. See mpirun(1). Use the normal mdrun(1) program for conventional single-threaded operations.\fP \&The mdrun program reads the run input file (\fB \-s\fR) \&and distributes the topology over nodes if needed. \&mdrun produces at least four output files. \&A single log file (\fB \-g\fR) is written, unless the option \&\fB \-seppot\fR is used, in which case each node writes a log file. \&The trajectory file (\fB \-o\fR), contains coordinates, velocities and \&optionally forces. \&The structure file (\fB \-c\fR) contains the coordinates and \&velocities of the last step. \&The energy file (\fB \-e\fR) contains energies, the temperature, \&pressure, etc, a lot of these things are also printed in the log file. \&Optionally coordinates can be written to a compressed trajectory file \&(\fB \-x\fR). \&The option \fB \-dhdl\fR is only used when free energy calculation is \&turned on. \&When mdrun is started using MPI with more than 1 node, parallelization \&is used. By default domain decomposition is used, unless the \fB \-pd\fR \&option is set, which selects particle decomposition. \&With domain decomposition, the spatial decomposition can be set \&with option \fB \-dd\fR. By default mdrun selects a good decomposition. \&The user only needs to change this when the system is very inhomogeneous. \&Dynamic load balancing is set with the option \fB \-dlb\fR, \&which can give a significant performance improvement, \&especially for inhomogeneous systems. The only disadvantage of \&dynamic load balancing is that runs are no longer binary reproducible, \&but in most cases this is not important. \&By default the dynamic load balancing is automatically turned on \&when the measured performance loss due to load imbalance is 5% or more. \&At low parallelization these are the only important options \&for domain decomposition. \&At high parallelization the options in the next two sections \&could be important for increasing the performace. \& \&When PME is used with domain decomposition, separate nodes can \&be assigned to do only the PME mesh calculation; \&this is computationally more efficient starting at about 12 nodes. \&The number of PME nodes is set with option \fB \-npme\fR, \&this can not be more than half of the nodes. \&By default mdrun makes a guess for the number of PME \&nodes when the number of nodes is larger than 11 or performance wise \¬ compatible with the PME grid x dimension. \&But the user should optimize npme. Performance statistics on this issue \&are written at the end of the log file. \&For good load balancing at high parallelization, the PME grid x and y \&dimensions should be divisible by the number of PME nodes \&(the simulation will run correctly also when this is not the case). \& \&This section lists all options that affect the domain decomposition. \& \&Option \fB \-rdd\fR can be used to set the required maximum distance \&for inter charge\-group bonded interactions. \&Communication for two\-body bonded interactions below the non\-bonded \&cut\-off distance always comes for free with the non\-bonded communication. \&Atoms beyond the non\-bonded cut\-off are only communicated when they have \&missing bonded interactions; this means that the extra cost is minor \&and nearly indepedent of the value of \fB \-rdd\fR. \&With dynamic load balancing option \fB \-rdd\fR also sets \&the lower limit for the domain decomposition cell sizes. \&By default \fB \-rdd\fR is determined by mdrun based on \&the initial coordinates. The chosen value will be a balance \&between interaction range and communication cost. \& \&When inter charge\-group bonded interactions are beyond \&the bonded cut\-off distance, mdrun terminates with an error message. \&For pair interactions and tabulated bonds \&that do not generate exclusions, this check can be turned off \&with the option \fB \-noddcheck\fR. \& \&When constraints are present, option \fB \-rcon\fR influences \&the cell size limit as well. \&Atoms connected by NC constraints, where NC is the LINCS order plus 1, \&should not be beyond the smallest cell size. A error message is \&generated when this happens and the user should change the decomposition \&or decrease the LINCS order and increase the number of LINCS iterations. \&By default mdrun estimates the minimum cell size required for P\-LINCS \&in a conservative fashion. For high parallelization it can be useful \&to set the distance required for P\-LINCS with the option \fB \-rcon\fR. \& \&The \fB \-dds\fR option sets the minimum allowed x, y and/or z scaling \&of the cells with dynamic load balancing. mdrun will ensure that \&the cells can scale down by at least this factor. This option is used \&for the automated spatial decomposition (when not using \fB \-dd\fR) \&as well as for determining the number of grid pulses, which in turn \&sets the minimum allowed cell size. Under certain circumstances \&the value of \fB \-dds\fR might need to be adjusted to account for \&high or low spatial inhomogeneity of the system. \& \&The option \fB \-gcom\fR can be used to only do global communication \&every n steps. \&This can improve performance for highly parallel simulations \&where this global communication step becomes the bottleneck. \&For a global thermostat and/or barostat the temperature \&and/or pressure will also only be updated every \-gcom steps. \&By default it is set to the minimum of nstcalcenergy and nstlist. \&With \fB \-rerun\fR an input trajectory can be given for which \&forces and energies will be (re)calculated. Neighbor searching will be \&performed for every frame, unless \fB nstlist\fR is zero \&(see the \fB .mdp\fR file). \&ED (essential dynamics) sampling is switched on by using the \fB \-ei\fR \&flag followed by an \fB .edi\fR file. \&The \fB .edi\fR file can be produced using options in the essdyn \&menu of the WHAT IF program. mdrun produces a \fB .edo\fR file that \&contains projections of positions, velocities and forces onto selected \&eigenvectors. \&When user\-defined potential functions have been selected in the \&\fB .mdp\fR file the \fB \-table\fR option is used to pass mdrun \&a formatted table with potential functions. The file is read from \&either the current directory or from the GMXLIB directory. \&A number of pre\-formatted tables are presented in the GMXLIB dir, \&for 6\-8, 6\-9, 6\-10, 6\-11, 6\-12 Lennard Jones potentials with \&normal Coulomb. \&When pair interactions are present a separate table for pair interaction \&functions is read using the \fB \-tablep\fR option. \&When tabulated bonded functions are present in the topology, \&interaction functions are read using the \fB \-tableb\fR option. \&For each different tabulated interaction type the table file name is \&modified in a different way: before the file extension an underscore is \&appended, then a b for bonds, an a for angles or a d for dihedrals \&and finally the table number of the interaction type. \&The options \fB \-px\fR and \fB \-pf\fR are used for writing pull COM \&coordinates and forces when pulling is selected \&in the \fB .mdp\fR file. \&With \fB \-multi\fR multiple systems are simulated in parallel. \&As many input files are required as the number of systems. \&The system number is appended to the run input and each output filename, \&for instance topol.tpr becomes topol0.tpr, topol1.tpr etc. \&The number of nodes per system is the total number of nodes \÷d by the number of systems. \&One use of this option is for NMR refinement: when distance \&or orientation restraints are present these can be ensemble averaged \&over all the systems. \&With \fB \-replex\fR replica exchange is attempted every given number \&of steps. The number of replicas is set with the \fB \-multi\fR option, \&see above. \&All run input files should use a different coupling temperature, \&the order of the files is not important. The random seed is set with \&\fB \-reseed\fR. The velocities are scaled and neighbor searching \&is performed after every exchange. \&Finally some experimental algorithms can be tested when the \&appropriate options have been given. Currently under \&investigation are: polarizability, and X\-Ray bombardments. \& \&The option \fB \-pforce\fR is useful when you suspect a simulation \&crashes due to too large forces. With this option coordinates and \&forces of atoms with a force larger than a certain value will \&be printed to stderr. \& \&Checkpoints containing the complete state of the system are written \&at regular intervals (option \fB \-cpt\fR) to the file \fB \-cpo\fR, \&unless option \fB \-cpt\fR is set to \-1. \&The previous checkpoint is backed up to \fB state_prev.cpt\fR to \&make sure that a recent state of the system is always available, \&even when the simulation is terminated while writing a checkpoint. \&With \fB \-cpnum\fR all checkpoint files are kept and appended \&with the step number. \&A simulation can be continued by reading the full state from file \&with option \fB \-cpi\fR. This option is intelligent in the way that \&if no checkpoint file is found, Gromacs just assumes a normal run and \&starts from the first step of the tpr file. By default the output \&will be appending to the existing output files. The checkpoint file \&contains checksums of all output files, such that you will never \&loose data when some output files are modified, corrupt or removed. \&There are three scenarios with \fB \-cpi\fR: \&* no files with matching names are present: new output files are written \&* all files are present with names and checksums matching those stored \&in the checkpoint file: files are appended \&* otherwise no files are modified and a fatal error is generated \&With \fB \-noappend\fR new output files are opened and the simulation \&part number is added to all output file names. \&Note that in all cases the checkpoint file itself is not renamed \&and will be overwritten, unless its name does not match \&the \fB \-cpo\fR option. \& \&With checkpointing the output is appended to previously written \&output files, unless \fB \-noappend\fR is used or none of the previous \&output files are present (except for the checkpoint file). \&The integrity of the files to be appended is verified using checksums \&which are stored in the checkpoint file. This ensures that output can \¬ be mixed up or corrupted due to file appending. When only some \&of the previous output files are present, a fatal error is generated \&and no old output files are modified and no new output files are opened. \&The result with appending will be the same as from a single run. \&The contents will be binary identical, unless you use a different number \&of nodes or dynamic load balancing or the FFT library uses optimizations \&through timing. \& \&With option \fB \-maxh\fR a simulation is terminated and a checkpoint \&file is written at the first neighbor search step where the run time \&exceeds \fB \-maxh\fR*0.99 hours. \& \&When mdrun receives a TERM signal, it will set nsteps to the current \&step plus one. When mdrun receives an INT signal (e.g. when ctrl+C is \&pressed), it will stop after the next neighbor search step \&(with nstlist=0 at the next step). \&In both cases all the usual output will be written to file. \&When running with MPI, a signal to one of the mdrun processes \&is sufficient, this signal should not be sent to mpirun or \&the mdrun process that is the parent of the others. \& \&When mdrun is started with MPI, it does not run niced by default. .SH FILES .BI "\-s" " topol.tpr" .B Input Run input file: tpr tpb tpa .BI "\-o" " traj.trr" .B Output Full precision trajectory: trr trj cpt .BI "\-x" " traj.xtc" .B Output, Opt. Compressed trajectory (portable xdr format) .BI "\-cpi" " state.cpt" .B Input, Opt. Checkpoint file .BI "\-cpo" " state.cpt" .B Output, Opt. Checkpoint file .BI "\-c" " confout.gro" .B Output Structure file: gro g96 pdb etc. .BI "\-e" " ener.edr" .B Output Energy file .BI "\-g" " md.log" .B Output Log file .BI "\-dhdl" " dhdl.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-field" " field.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-table" " table.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-tablep" " tablep.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-tableb" " table.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-rerun" " rerun.xtc" .B Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt .BI "\-tpi" " tpi.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-tpid" " tpidist.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-ei" " sam.edi" .B Input, Opt. ED sampling input .BI "\-eo" " sam.edo" .B Output, Opt. ED sampling output .BI "\-j" " wham.gct" .B Input, Opt. General coupling stuff .BI "\-jo" " bam.gct" .B Output, Opt. General coupling stuff .BI "\-ffout" " gct.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-devout" " deviatie.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-runav" " runaver.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-px" " pullx.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-pf" " pullf.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-mtx" " nm.mtx" .B Output, Opt. Hessian matrix .BI "\-dn" " dipole.ndx" .B Output, Opt. Index file .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 0" Set the nicelevel .BI "\-deffnm" " string" " " Set the default filename for all file options .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR .BI "\-[no]pd" "no " Use particle decompostion .BI "\-dd" " vector" " 0 0 0" Domain decomposition grid, 0 is optimize .BI "\-nt" " int" " 0" Number of threads to start (0 is guess) .BI "\-npme" " int" " \-1" Number of separate nodes to be used for PME, \-1 is guess .BI "\-ddorder" " enum" " interleave" DD node order: \fB interleave\fR, \fB pp_pme\fR or \fB cartesian\fR .BI "\-[no]ddcheck" "yes " Check for all bonded interactions with DD .BI "\-rdd" " real" " 0 " The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates .BI "\-rcon" " real" " 0 " Maximum distance for P\-LINCS (nm), 0 is estimate .BI "\-dlb" " enum" " auto" Dynamic load balancing (with DD): \fB auto\fR, \fB no\fR or \fB yes\fR .BI "\-dds" " real" " 0.8 " Minimum allowed dlb scaling of the DD cell size .BI "\-gcom" " int" " \-1" Global communication frequency .BI "\-[no]v" "no " Be loud and noisy .BI "\-[no]compact" "yes " Write a compact log file .BI "\-[no]seppot" "no " Write separate V and dVdl terms for each interaction type and node to the log file(s) .BI "\-pforce" " real" " \-1 " Print all forces larger than this (kJ/mol nm) .BI "\-[no]reprod" "no " Try to avoid optimizations that affect binary reproducibility .BI "\-cpt" " real" " 15 " Checkpoint interval (minutes) .BI "\-[no]cpnum" "no " Keep and number checkpoint files .BI "\-[no]append" "yes " Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names .BI "\-maxh" " real" " \-1 " Terminate after 0.99 times this time (hours) .BI "\-multi" " int" " 0" Do multiple simulations in parallel .BI "\-replex" " int" " 0" Attempt replica exchange every steps .BI "\-reseed" " int" " \-1" Seed for replica exchange, \-1 is generate a seed .BI "\-[no]ionize" "no " Do a simulation including the effect of an X\-Ray bombardment on your system .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>. debian/man/g_kinetics.10000664000000000000000000001165111124354443012151 0ustar .TH "G_KINETICS" "1" "20 Aug 2008" "GROMACS suite, Version 3.3" .SH NAME g_kinetics \- estimate rate constants .SH SYNOPSIS .B g_kinetics .BI "\-f" " temp.xvg " .BI "\-d" " data.xvg " .BI "\-o" " ft_all.xvg " .BI "\-g" " remd.log " .BI "\-m" " melt.xvg " .I [other options...] .SH DESCRIPTION .B g_kinetics reads two xvg files, each one containing data for N replicas. The first file contains the temperature of each replica at each timestep and the second contains real values that can be interpreted as an indicator for folding. If the value in the file is larger than the cutoff it is taken to be unfolded and the other way around.[PAR] From these data an estimate of the forward and backward rate constants for folding is made at a reference temperature. In addition, a theoretical melting curve and free energy as a function of temperature are printed in an xvg file. The user can give a max value to be regarded as intermediate (\fI\-ucut\fP), which, when given will trigger the use of an intermediate state in the algorithm to be defined as those structures that have cutoff < DATA < ucut. Structures with DATA values larger than ucut will not be regarded as potential folders. In this case 8 parameters are optimized. The average fraction folded is printed in an xvg file together with the fit to it. If an intermediate is used a further file will show the build of the intermediate and the fit to that process. The program can also be used with continuous variables (by setting \fI\-nodiscrete\fP). In this case kinetics of other processes can be studied. This is very much a work in progress and hence the manual (this information) is lagging behind somewhat. .SH FILES .nf Option Filename Type Description ------------------------------------------------------------ \-f temp.xvg Input xvgr/xmgr file \-d data.xvg Input xvgr/xmgr file \-d2 data2.xvg Input, Opt. xvgr/xmgr file \-o ft_all.xvg Output xvgr/xmgr file \-o2 it_all.xvg Output, Opt. xvgr/xmgr file \-o3 ft_repl.xvg Output, Opt. xvgr/xmgr file \-ee err_est.xvg Output, Opt. xvgr/xmgr file \-g remd.log Output Log file \-m melt.xvg Output xvgr/xmgr file .fi .SH OPTIONS .nf Option Type Value Description ------------------------------------------------------ \-[no]h bool no Print help info and quit \-[no]X bool no Use dialog box GUI to edit command line options \-nice int 19 Set the nicelevel \-tu enum ps Time unit: ps, fs, ns, us, ms or s \-[no]w bool no View output xvg, xpm, eps and pdb files \-[no]xvgr bool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program \-[no]time bool yes Expect a time in the input \-b real 0 First time to read from set \-e real 0 Last time to read from set \-bfit real \-1 Time to start the fit from \-efit real \-1 Time to end the fit \-T real 298.15 Reference temperature for computing rate constants \-n int 1 Read data for # replicas. Only necessary when files are written in xmgrace format using @type and & as delimiters. \-cut real 0.2 Cut-off (max) value for regarding a structure as folded \-ucut real 0 Cut-off (max) value for regarding a structure as intermediate (if not folded) \-euf real 10 Initial guess for energy of activation for folding (kJ/mole) \-efu real 30 Initial guess for energy of activation for unfolding (kJ/mole) \-ei real 10 Initial guess for energy of activation for intermediates (kJ/mole) \-maxiter int 100 Max number of iterations \-[no]back bool yes Take the back reaction into account \-tol real 0.001 Absolute tolerance for convergence of the Nelder and Mead simplex algorithm \-skip int 0 Skip points in the output xvg file \-[no]split bool yes Estimate error by splitting the number of replicas in two and refitting \-[no]sum bool yes Average folding before computing chi^2 \-[no]discrete bool yes Use a discrete folding criterium (F <-> U) or a continuous one \-mult int 1 Factor to multiply the data with before discretization .fi .SH SEE ALSO .BR gromacs (7) .PP More information about the \fBGROMACS\fR suite is available in \fI/usr/share/doc/gromacs\fR or at \fI\%http://www.gromacs.org/\fR. .PP Implementation details have been published in Phys. Rev. Lett. 96, 238102 (2006), <\fI\%http://dx.doi.org/10.1103/PhysRevLett.96.238102\fR>. debian/man/xplor2gmx.10000664000000000000000000000165411542010054011765 0ustar .TH "xplor2gmx" "1" "13 Oct 2008" "GROMACS suite, Version 4.0" .SH NAME xplor2gmx \- Convert XPLOR distance restraints to Gromacs format .SH SYNOPSIS \f3xplor2gmx\fP .BI "(residue offset)" "" .BI " input.pdb " "" .SH DESCRIPTION .B xplor2gmx reads an XPLOR input file with distance restraint data as sometimes is found in the pdb database (http://www.pdb.org). From this input file dihedral restrints should be removed, such that only distance restraints are left. The script can handle ambiguous restraints. It converts the distance restraints to GROMACS format. A restraints file (.dat) should be provided on STDIN, and a suitable output file (.itp) is sent to STDOUT. .SH EXAMPLES xplor2gmx.pl 33 conf.pdb < restraints.dat > disre.itp .SH OPTIONS .B xplor2gmx requires two command line options: first, the residue offset (integer); second, the .pdb filename. The pdb file must have correct atom numbers. .SH SEE ALSO .BR gromacs (7) debian/man/mdrun_mpi.mpich.10000664000000000000000000004302611542010054013113 0ustar .TH mdrun_mpi 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5" .SH NAME mdrun_mpi - performs a simulation, do a normal mode analysis or an energy minimization across multiple CPUs or systems .B VERSION 4.5 .SH SYNOPSIS \f3mdrun_mpi\fP .BI "\-s" " topol.tpr " .BI "\-o" " traj.trr " .BI "\-x" " traj.xtc " .BI "\-cpi" " state.cpt " .BI "\-cpo" " state.cpt " .BI "\-c" " confout.gro " .BI "\-e" " ener.edr " .BI "\-g" " md.log " .BI "\-dhdl" " dhdl.xvg " .BI "\-field" " field.xvg " .BI "\-table" " table.xvg " .BI "\-tablep" " tablep.xvg " .BI "\-tableb" " table.xvg " .BI "\-rerun" " rerun.xtc " .BI "\-tpi" " tpi.xvg " .BI "\-tpid" " tpidist.xvg " .BI "\-ei" " sam.edi " .BI "\-eo" " sam.edo " .BI "\-j" " wham.gct " .BI "\-jo" " bam.gct " .BI "\-ffout" " gct.xvg " .BI "\-devout" " deviatie.xvg " .BI "\-runav" " runaver.xvg " .BI "\-px" " pullx.xvg " .BI "\-pf" " pullf.xvg " .BI "\-mtx" " nm.mtx " .BI "\-dn" " dipole.ndx " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .BI "\-deffnm" " string " .BI "\-xvg" " enum " .BI "\-[no]pd" "" .BI "\-dd" " vector " .BI "\-nt" " int " .BI "\-npme" " int " .BI "\-ddorder" " enum " .BI "\-[no]ddcheck" "" .BI "\-rdd" " real " .BI "\-rcon" " real " .BI "\-dlb" " enum " .BI "\-dds" " real " .BI "\-gcom" " int " .BI "\-[no]v" "" .BI "\-[no]compact" "" .BI "\-[no]seppot" "" .BI "\-pforce" " real " .BI "\-[no]reprod" "" .BI "\-cpt" " real " .BI "\-[no]cpnum" "" .BI "\-[no]append" "" .BI "\-maxh" " real " .BI "\-multi" " int " .BI "\-replex" " int " .BI "\-reseed" " int " .BI "\-[no]ionize" "" .SH DESCRIPTION \&The mdrun program is the main computational chemistry engine \&within GROMACS. Obviously, it performs Molecular Dynamics simulations, \&but it can also perform Stochastic Dynamics, Energy Minimization, \&test particle insertion or (re)calculation of energies. \&Normal mode analysis is another option. In this case mdrun \&builds a Hessian matrix from single conformation. \&For usual Normal Modes\-like calculations, make sure that \&the structure provided is properly energy\-minimized. \&The generated matrix can be diagonalized by g_nmeig. \fIThis version of the program will only run while using the MPICH parallel computing library. See mpirun(1). Use the normal mdrun(1) program for conventional single-threaded operations.\fP \&The mdrun program reads the run input file (\fB \-s\fR) \&and distributes the topology over nodes if needed. \&mdrun produces at least four output files. \&A single log file (\fB \-g\fR) is written, unless the option \&\fB \-seppot\fR is used, in which case each node writes a log file. \&The trajectory file (\fB \-o\fR), contains coordinates, velocities and \&optionally forces. \&The structure file (\fB \-c\fR) contains the coordinates and \&velocities of the last step. \&The energy file (\fB \-e\fR) contains energies, the temperature, \&pressure, etc, a lot of these things are also printed in the log file. \&Optionally coordinates can be written to a compressed trajectory file \&(\fB \-x\fR). \&The option \fB \-dhdl\fR is only used when free energy calculation is \&turned on. \&When mdrun is started using MPI with more than 1 node, parallelization \&is used. By default domain decomposition is used, unless the \fB \-pd\fR \&option is set, which selects particle decomposition. \&With domain decomposition, the spatial decomposition can be set \&with option \fB \-dd\fR. By default mdrun selects a good decomposition. \&The user only needs to change this when the system is very inhomogeneous. \&Dynamic load balancing is set with the option \fB \-dlb\fR, \&which can give a significant performance improvement, \&especially for inhomogeneous systems. The only disadvantage of \&dynamic load balancing is that runs are no longer binary reproducible, \&but in most cases this is not important. \&By default the dynamic load balancing is automatically turned on \&when the measured performance loss due to load imbalance is 5% or more. \&At low parallelization these are the only important options \&for domain decomposition. \&At high parallelization the options in the next two sections \&could be important for increasing the performace. \& \&When PME is used with domain decomposition, separate nodes can \&be assigned to do only the PME mesh calculation; \&this is computationally more efficient starting at about 12 nodes. \&The number of PME nodes is set with option \fB \-npme\fR, \&this can not be more than half of the nodes. \&By default mdrun makes a guess for the number of PME \&nodes when the number of nodes is larger than 11 or performance wise \¬ compatible with the PME grid x dimension. \&But the user should optimize npme. Performance statistics on this issue \&are written at the end of the log file. \&For good load balancing at high parallelization, the PME grid x and y \&dimensions should be divisible by the number of PME nodes \&(the simulation will run correctly also when this is not the case). \& \&This section lists all options that affect the domain decomposition. \& \&Option \fB \-rdd\fR can be used to set the required maximum distance \&for inter charge\-group bonded interactions. \&Communication for two\-body bonded interactions below the non\-bonded \&cut\-off distance always comes for free with the non\-bonded communication. \&Atoms beyond the non\-bonded cut\-off are only communicated when they have \&missing bonded interactions; this means that the extra cost is minor \&and nearly indepedent of the value of \fB \-rdd\fR. \&With dynamic load balancing option \fB \-rdd\fR also sets \&the lower limit for the domain decomposition cell sizes. \&By default \fB \-rdd\fR is determined by mdrun based on \&the initial coordinates. The chosen value will be a balance \&between interaction range and communication cost. \& \&When inter charge\-group bonded interactions are beyond \&the bonded cut\-off distance, mdrun terminates with an error message. \&For pair interactions and tabulated bonds \&that do not generate exclusions, this check can be turned off \&with the option \fB \-noddcheck\fR. \& \&When constraints are present, option \fB \-rcon\fR influences \&the cell size limit as well. \&Atoms connected by NC constraints, where NC is the LINCS order plus 1, \&should not be beyond the smallest cell size. A error message is \&generated when this happens and the user should change the decomposition \&or decrease the LINCS order and increase the number of LINCS iterations. \&By default mdrun estimates the minimum cell size required for P\-LINCS \&in a conservative fashion. For high parallelization it can be useful \&to set the distance required for P\-LINCS with the option \fB \-rcon\fR. \& \&The \fB \-dds\fR option sets the minimum allowed x, y and/or z scaling \&of the cells with dynamic load balancing. mdrun will ensure that \&the cells can scale down by at least this factor. This option is used \&for the automated spatial decomposition (when not using \fB \-dd\fR) \&as well as for determining the number of grid pulses, which in turn \&sets the minimum allowed cell size. Under certain circumstances \&the value of \fB \-dds\fR might need to be adjusted to account for \&high or low spatial inhomogeneity of the system. \& \&The option \fB \-gcom\fR can be used to only do global communication \&every n steps. \&This can improve performance for highly parallel simulations \&where this global communication step becomes the bottleneck. \&For a global thermostat and/or barostat the temperature \&and/or pressure will also only be updated every \-gcom steps. \&By default it is set to the minimum of nstcalcenergy and nstlist. \&With \fB \-rerun\fR an input trajectory can be given for which \&forces and energies will be (re)calculated. Neighbor searching will be \&performed for every frame, unless \fB nstlist\fR is zero \&(see the \fB .mdp\fR file). \&ED (essential dynamics) sampling is switched on by using the \fB \-ei\fR \&flag followed by an \fB .edi\fR file. \&The \fB .edi\fR file can be produced using options in the essdyn \&menu of the WHAT IF program. mdrun produces a \fB .edo\fR file that \&contains projections of positions, velocities and forces onto selected \&eigenvectors. \&When user\-defined potential functions have been selected in the \&\fB .mdp\fR file the \fB \-table\fR option is used to pass mdrun \&a formatted table with potential functions. The file is read from \&either the current directory or from the GMXLIB directory. \&A number of pre\-formatted tables are presented in the GMXLIB dir, \&for 6\-8, 6\-9, 6\-10, 6\-11, 6\-12 Lennard Jones potentials with \&normal Coulomb. \&When pair interactions are present a separate table for pair interaction \&functions is read using the \fB \-tablep\fR option. \&When tabulated bonded functions are present in the topology, \&interaction functions are read using the \fB \-tableb\fR option. \&For each different tabulated interaction type the table file name is \&modified in a different way: before the file extension an underscore is \&appended, then a b for bonds, an a for angles or a d for dihedrals \&and finally the table number of the interaction type. \&The options \fB \-px\fR and \fB \-pf\fR are used for writing pull COM \&coordinates and forces when pulling is selected \&in the \fB .mdp\fR file. \&With \fB \-multi\fR multiple systems are simulated in parallel. \&As many input files are required as the number of systems. \&The system number is appended to the run input and each output filename, \&for instance topol.tpr becomes topol0.tpr, topol1.tpr etc. \&The number of nodes per system is the total number of nodes \÷d by the number of systems. \&One use of this option is for NMR refinement: when distance \&or orientation restraints are present these can be ensemble averaged \&over all the systems. \&With \fB \-replex\fR replica exchange is attempted every given number \&of steps. The number of replicas is set with the \fB \-multi\fR option, \&see above. \&All run input files should use a different coupling temperature, \&the order of the files is not important. The random seed is set with \&\fB \-reseed\fR. The velocities are scaled and neighbor searching \&is performed after every exchange. \&Finally some experimental algorithms can be tested when the \&appropriate options have been given. Currently under \&investigation are: polarizability, and X\-Ray bombardments. \& \&The option \fB \-pforce\fR is useful when you suspect a simulation \&crashes due to too large forces. With this option coordinates and \&forces of atoms with a force larger than a certain value will \&be printed to stderr. \& \&Checkpoints containing the complete state of the system are written \&at regular intervals (option \fB \-cpt\fR) to the file \fB \-cpo\fR, \&unless option \fB \-cpt\fR is set to \-1. \&The previous checkpoint is backed up to \fB state_prev.cpt\fR to \&make sure that a recent state of the system is always available, \&even when the simulation is terminated while writing a checkpoint. \&With \fB \-cpnum\fR all checkpoint files are kept and appended \&with the step number. \&A simulation can be continued by reading the full state from file \&with option \fB \-cpi\fR. This option is intelligent in the way that \&if no checkpoint file is found, Gromacs just assumes a normal run and \&starts from the first step of the tpr file. By default the output \&will be appending to the existing output files. The checkpoint file \&contains checksums of all output files, such that you will never \&loose data when some output files are modified, corrupt or removed. \&There are three scenarios with \fB \-cpi\fR: \&* no files with matching names are present: new output files are written \&* all files are present with names and checksums matching those stored \&in the checkpoint file: files are appended \&* otherwise no files are modified and a fatal error is generated \&With \fB \-noappend\fR new output files are opened and the simulation \&part number is added to all output file names. \&Note that in all cases the checkpoint file itself is not renamed \&and will be overwritten, unless its name does not match \&the \fB \-cpo\fR option. \& \&With checkpointing the output is appended to previously written \&output files, unless \fB \-noappend\fR is used or none of the previous \&output files are present (except for the checkpoint file). \&The integrity of the files to be appended is verified using checksums \&which are stored in the checkpoint file. This ensures that output can \¬ be mixed up or corrupted due to file appending. When only some \&of the previous output files are present, a fatal error is generated \&and no old output files are modified and no new output files are opened. \&The result with appending will be the same as from a single run. \&The contents will be binary identical, unless you use a different number \&of nodes or dynamic load balancing or the FFT library uses optimizations \&through timing. \& \&With option \fB \-maxh\fR a simulation is terminated and a checkpoint \&file is written at the first neighbor search step where the run time \&exceeds \fB \-maxh\fR*0.99 hours. \& \&When mdrun receives a TERM signal, it will set nsteps to the current \&step plus one. When mdrun receives an INT signal (e.g. when ctrl+C is \&pressed), it will stop after the next neighbor search step \&(with nstlist=0 at the next step). \&In both cases all the usual output will be written to file. \&When running with MPI, a signal to one of the mdrun processes \&is sufficient, this signal should not be sent to mpirun or \&the mdrun process that is the parent of the others. \& \&When mdrun is started with MPI, it does not run niced by default. .SH FILES .BI "\-s" " topol.tpr" .B Input Run input file: tpr tpb tpa .BI "\-o" " traj.trr" .B Output Full precision trajectory: trr trj cpt .BI "\-x" " traj.xtc" .B Output, Opt. Compressed trajectory (portable xdr format) .BI "\-cpi" " state.cpt" .B Input, Opt. Checkpoint file .BI "\-cpo" " state.cpt" .B Output, Opt. Checkpoint file .BI "\-c" " confout.gro" .B Output Structure file: gro g96 pdb etc. .BI "\-e" " ener.edr" .B Output Energy file .BI "\-g" " md.log" .B Output Log file .BI "\-dhdl" " dhdl.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-field" " field.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-table" " table.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-tablep" " tablep.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-tableb" " table.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-rerun" " rerun.xtc" .B Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt .BI "\-tpi" " tpi.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-tpid" " tpidist.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-ei" " sam.edi" .B Input, Opt. ED sampling input .BI "\-eo" " sam.edo" .B Output, Opt. ED sampling output .BI "\-j" " wham.gct" .B Input, Opt. General coupling stuff .BI "\-jo" " bam.gct" .B Output, Opt. General coupling stuff .BI "\-ffout" " gct.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-devout" " deviatie.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-runav" " runaver.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-px" " pullx.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-pf" " pullf.xvg" .B Output, Opt. xvgr/xmgr file .BI "\-mtx" " nm.mtx" .B Output, Opt. Hessian matrix .BI "\-dn" " dipole.ndx" .B Output, Opt. Index file .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 0" Set the nicelevel .BI "\-deffnm" " string" " " Set the default filename for all file options .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR .BI "\-[no]pd" "no " Use particle decompostion .BI "\-dd" " vector" " 0 0 0" Domain decomposition grid, 0 is optimize .BI "\-nt" " int" " 0" Number of threads to start (0 is guess) .BI "\-npme" " int" " \-1" Number of separate nodes to be used for PME, \-1 is guess .BI "\-ddorder" " enum" " interleave" DD node order: \fB interleave\fR, \fB pp_pme\fR or \fB cartesian\fR .BI "\-[no]ddcheck" "yes " Check for all bonded interactions with DD .BI "\-rdd" " real" " 0 " The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates .BI "\-rcon" " real" " 0 " Maximum distance for P\-LINCS (nm), 0 is estimate .BI "\-dlb" " enum" " auto" Dynamic load balancing (with DD): \fB auto\fR, \fB no\fR or \fB yes\fR .BI "\-dds" " real" " 0.8 " Minimum allowed dlb scaling of the DD cell size .BI "\-gcom" " int" " \-1" Global communication frequency .BI "\-[no]v" "no " Be loud and noisy .BI "\-[no]compact" "yes " Write a compact log file .BI "\-[no]seppot" "no " Write separate V and dVdl terms for each interaction type and node to the log file(s) .BI "\-pforce" " real" " \-1 " Print all forces larger than this (kJ/mol nm) .BI "\-[no]reprod" "no " Try to avoid optimizations that affect binary reproducibility .BI "\-cpt" " real" " 15 " Checkpoint interval (minutes) .BI "\-[no]cpnum" "no " Keep and number checkpoint files .BI "\-[no]append" "yes " Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names .BI "\-maxh" " real" " \-1 " Terminate after 0.99 times this time (hours) .BI "\-multi" " int" " 0" Do multiple simulations in parallel .BI "\-replex" " int" " 0" Attempt replica exchange every steps .BI "\-reseed" " int" " \-1" Seed for replica exchange, \-1 is generate a seed .BI "\-[no]ionize" "no " Do a simulation including the effect of an X\-Ray bombardment on your system .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>. debian/gromacs-dev.dirs0000664000000000000000000000006411011457627012266 0ustar usr/lib usr/share/gromacs usr/share/doc/gromacs-dev debian/changelog0000664000000000000000000006650012253224244011051 0ustar gromacs (4.6.5-1build1) trusty; urgency=medium * No-change rebuild for libopenmpi1.3 -> libopenmpi1.6 transition. -- Logan Rosen Sat, 14 Dec 2013 22:57:15 -0500 gromacs (4.6.5-1) unstable; urgency=low * New upstream release. * rules: Override autodetection of CPU extensions on amd64 and i386; force to SSE2 only, and provide new DEB_BUILD_OPTIONS=cpuopt flag to re-enable autodetection for local builds. (Closes: #725013) * rules: Fix misplaced COPYING symlink in gromacs-data. * source/lintian-overrides: Add overrides for outstanding lintian bugs #729096 (newer policy version), #724866 (libmpich-dev not virtual). * patches/20_manpages.patch: Fix formatting errors in the NAME line of several man pages. * gromacs-data.doc-base: Change root to getting_started.html. The shipped HTML documentation is slowly being eliminated in favor of a wiki on gromacs.org. -- Nicholas Breen Mon, 09 Dec 2013 10:40:36 -0800 gromacs (4.6.3-4) unstable; urgency=low * control: Add versioned Build-Depends on libmpich-dev (>= 3), to prevent build failures on architectures where that still represents the old MPICH version 1. * rules: More mpich2 -> mpich replacements. -- Nicholas Breen Sun, 29 Sep 2013 21:39:46 -0700 gromacs (4.6.3-3) unstable; urgency=low * control: - Move Replaces/Breaks to MPI packages instead. (Closes: #718001) - Move all mpich2 dependencies to new mpich (v3) package names. * control, rules: - Add ppc64 to list of supported architectures for gromacs-openmpi. - Temporarily add use of "chrpath -d" on gromacs-mpich binaries, due to mpicc.mpich setting RPATH unconditionally (see #724864). -- Nicholas Breen Sun, 29 Sep 2013 16:30:43 -0700 gromacs (4.6.3-2) unstable; urgency=low * control: - Add B-Ds for external BLAS/LAPACK libraries. - Have -dev Replaces/Breaks earlier versions of -openmpi/-mpich to handle file move. (Closes: #718001) - For gromacs, remove Conflicts with a long-obsolete (before squeeze) version of radiance, and add Suggests on pymol for visualization. * rules: Specify verbose output from CMake. -- Nicholas Breen Sun, 11 Aug 2013 13:05:19 -0700 gromacs (4.6.3-1) unstable; urgency=low * New upstream release; post-freeze, uploading to unstable. * rules, control: Remove special provisions for FORTRAN on Alpha. * rules: Update configuration parameters. * rules, patches/12_copyright-file.patch: Avoid duplication of copyright information into two files, but provide a link to keep both filenames. * control: Drop obsolete B-D on lesstif2-dev. (Closes: #714753) * rules: Move .so symlinks for MPI libraries from -dev to their respective packages, to ensure that they can't be installed without their targets. * control: Update SCM links. -- Nicholas Breen Fri, 05 Jul 2013 13:57:44 -0700 gromacs (4.6-1) experimental; urgency=low * New upstream release, targeted at experimental during freeze. - Remove patches/10_release-4-5-patches.patch (obsolete), 31_manpages.patch (incorporated upstream). - Update lintian overrides. -- Nicholas Breen Mon, 25 Feb 2013 10:47:14 -0800 gromacs (4.5.5-2) unstable; urgency=low [ Andreas Tille ] * debian/upstream: - copied citations from tasks/bio to debian/upstream - make last citation conform to BibTeX syntax [ Nicholas Breen ] * Update to current release-4.5-patches git (f361fa9c) via addition of patches/10_release-4.5-patches.patch. * source/format: Move to 3.0 (quilt). Adjust patches accordingly. * control: Remove specific listing of MPI packages from description of gromacs-dev. (Closes: #644820) Update maintainer address and drop DMUA stanza. Drop Build-Depends on dpatch, add on hardening-wrapper. Update to S-V 3.9.3, no packaging changes required. * rules, README.source: Remove dpatch cruft. * rules: Apply compiler hardening flags with hardening-wrapper. * patches/*: Tidy up with DEP-3 headers. * control, rules: Update list of architectures for gromacs-openmpi, adding armel, armhf, powerpcspe, and sparc64. -- Nicholas Breen Sat, 09 Jun 2012 11:42:56 -0700 gromacs (4.5.5-1) unstable; urgency=low * New upstream release. - Remove patches/30_git_release-4.5-patches.dpatch. - man/g_dos.1: Create man page for new binary. * rules: Add build-arch/build-indep targets. Add preliminary support for building GPU-accelerated binaries: set DEB_BUILD_OPTIONS=gpu to try it. * patches/31_manpages.dpatch: Update. -- Nicholas Breen Wed, 21 Sep 2011 19:10:08 -0700 gromacs (4.5.4-2) unstable; urgency=low * control: remove obsolete Build-Depends and Suggests on libice-dev, libsm-dev, libxext-dev, libxp-dev, libxt-dev. Update Standards-Version to 3.9.2. * patches/30_git_release-4.5-patches.dpatch: Routine update from upstream git, to commit 873563ef of 22 April 2011. * patches/31_manpages.dpatch: Various minor spelling and header fixes. * lintian-overrides.gromacs: Remove checks no longer needed, per #120323. * rules: Switch to using dh_lintian. -- Nicholas Breen Mon, 25 Apr 2011 13:47:00 -0700 gromacs (4.5.4-1) unstable; urgency=low * New upstream release. * Remove gromacs-lam transitional package. * man/g_options.1: Create man page for new binary. * lintian-overrides.gromacs-data: Override script-not-executable for demo scripts not in $PATH. -- Nicholas Breen Mon, 21 Mar 2011 19:59:54 -0700 gromacs (4.5.3-1) unstable; urgency=low * New upstream release. * Force -DGMX_X11=ON to build ngmx. (Closes: #603327) -- Nicholas Breen Sat, 13 Nov 2010 12:02:17 -0800 gromacs (4.5.2-1) unstable; urgency=low * Major new upstream release. * All patches incorporated upstream and removed, except the Debian- specific bug reporting portion of 11_readme.dpatch. * man/gromacs.7: incorporated upstream, removed from Debian patch. * man/luck.1: Rename to g_luck.1 and edit to reflect new name. * man/mdrun_mpi.*.1: Resynchronize with upstream mdrun.1. * watch: Update to recognize -betaX tarballs and ignore -GPU builds. * rules: Convert from autotools to new CMake build system. * control: - Add Build-Depends on libxml2-dev. - Update Standards-Version to 3.9.1. - Replace Conflicts: with Breaks:. -- Nicholas Breen Wed, 03 Nov 2010 17:39:52 -0700 gromacs (4.0.7-3) unstable; urgency=low * New patch 03_autoconf_bashisms.dpatch: Eliminate two bashisms (test == instead of =) in configure.ac, permitting use with dash instead. * patches/30_git_release-4.0-patches.dpatch: Update to commit 36df279783944c11d1ba43936ea820f8e6003ffd. -- Nicholas Breen Tue, 25 May 2010 19:30:48 -0700 gromacs (4.0.7-2) unstable; urgency=low * rules: - Drop chrpath workaround, underlying bug solved with mpich2 1.2.1.1-2. - Add sparc to list of architectures for -openmpi. * control: - Per above. - Set DM-Upload-Allowed: yes. - Update Standards-Version to 3.8.4. - Add ${misc:Depends} for Lintian, except for -data and -lam which receive overrides instead. * gromacs-parallel.README.Debian.in: Remove reference to LAM-MPI. * patches/30_git_release-4.0-patches.dpatch: Update to commit 444432a51f87f003fc6e7098f9e07a2a2d142c64. * source/format: Create and set explicitly to 1.0. * source/lintian-overrides: Override debhelper-but-no-misc-depends for gromacs-data and gromacs-lam. -- Nicholas Breen Tue, 13 Apr 2010 23:33:27 -0700 gromacs (4.0.7-1) unstable; urgency=low * New upstream release. * patches/30_git_release-4.0-patches.dpatch: Empty out, replace with fresh pull starting at the 4.0.7 release; current to git commit 665dce86638df8ac1062b0b022d7827ea0f11788. -- Nicholas Breen Thu, 31 Dec 2009 16:43:03 -0800 gromacs (4.0.5-5) unstable; urgency=low * Transition to only the two supported MPI implementations: - gromacs-mpich now builds against MPICH2, not MPICH1. - gromacs-lam replaced with a dummy package installing gromacs- openmpi on all supported architectures, -mpich on the holdouts. - Update documentation accordingly. * patches/30_git_release-4.0-patches.dpatch: Pull from upstream git repository, release-4.0-patches branch. Current to git commit 37a4dd35fec7579ca7faca25c62c71cf1d8e1621, 29 Nov. 2009. * patches/21_makefile_dups.dpatch: Delete, incorporated above (commit c93db8511af09c144fe4b2b8f57b14a5ad1e6cc7). * compat: Update to debhelper v7 mode. - rules: Replace dh_clean -k with dh_prep. - control: Adjust Build-Depends to debhelper (>= 7.0.0). * copyright: Increment year. * rules: Use chrpath to eliminate RPATH from MPICH2-compiled binaries. This is a workaround for a libmpich2-dev bug, #558960. - control: Add chrpath to Build-Depends. * rules: Add -Wl,--as-needed to LDFLAGS. -- Nicholas Breen Mon, 30 Nov 2009 16:18:34 -0800 gromacs (4.0.5-4) unstable; urgency=low * patches/21_makefile_dups.dpatch: Eliminate duplicated files in the installation list of include/Makefile.am. Automake 1.11 now passes multiple files to `install' at once, causing failures when one name is given twice. (Closes: #543059) * control: Increment S-V to 3.8.3. No changes required. * rules: Remove obsolete --disable-nice option from *_CONFIG_PARAMS. * man/gromacs.7: Update macros for lintian cleanliness. -- Nicholas Breen Tue, 25 Aug 2009 12:30:15 -0700 gromacs (4.0.5-3) unstable; urgency=low * patches/20_altivec_kernel.dpatch: Extend patch to cover nb_kernel_ppc_altivec.c, which does not include the same headers. * control: Increment Standards-Version to 3.8.2. No packaging changes required. -- Nicholas Breen Wed, 24 Jun 2009 17:21:26 -0700 gromacs (4.0.5-2) unstable; urgency=low * patches/20_altivec_kernel.dpatch: Resolve FTBFS on AltiVec-enabled PPC builds caused by use of "restrict" keyword, which GCC does not normally accept unless in C99 mode. Reported upstream at http://bugzilla.gromacs.org/show_bug.cgi?id=324 -- Nicholas Breen Sun, 17 May 2009 15:52:53 -0700 gromacs (4.0.5-1) unstable; urgency=low * New upstream release. * debian/control: Bump Standards-Version to 3.8.1. No packaging changes required. * debian/control: Replace svn+ssh:// URI with svn:// . * debian/copyright: Replace "(C)" with "Copyright", update dates. * debian/rules: #452047 rears its ugly head again! Add LDFLAGS to -lam and -openmpi builds with -L arguments to their respective library directories, exclusive of update-alternatives trickery, in order to prevent accidental cross-linking. Thanks again to Manuel Prinz. (Closes: #526266) -- Nicholas Breen Mon, 11 May 2009 18:15:11 -0700 gromacs (4.0.4-1) unstable; urgency=low * New upstream release. * patches/05_lt_init.dpatch: Add LT_INIT to configure.ac so that the libtool script can find its version. Necessary for current Ubuntu build environment. Patch courtesy of James Westby. -- Nicholas Breen Sat, 28 Feb 2009 16:45:25 -0800 gromacs (4.0.3-1) unstable; urgency=low * New upstream release. * Remove obsoleted patches 40, 41, 50, 51, 52. -- Nicholas Breen Mon, 19 Jan 2009 13:35:23 -0800 gromacs (4.0.2-2) unstable; urgency=low * debian/*.postinst: Resort update-alternatives priorities for the MPI packages to follow the newly proposed priorities of the individual MPI implementations themselves, OpenMPI > MPICH > LAM. * New patches: - 40_hppa_asm.dpatch: Attempt to correct FTBFS on HPPA inline ASM code by replacing an undefined variable. (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=260) - 41_sprintf.dpatch: Replace sprintf calls relying on undefined behavior with proper, portable code. Problem identified by Kees Cook: http://lists.debian.org/debian-devel/2008/12/msg01079.html - 50_type2bonds.dpatch: Fix grompp freeze when using type 2 bonds (G96) and all-angle constraints. (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=261) - 51_mshift.dpatch: When running mdrun on multiple processors, it will crash under certain circumstances when an error is generated but there is no log file attached to that specific process. This was triggered by some incorrect "inconsistent shift" warning messages. Both problems are corrected by this patch. (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=267) - 52_ia64_single_pointer.dpatch: Test for non-zero pointer in IA64 single-precision kernel when writing to log file. Pointer is zero on non-master MPI processes, and would previously segfault. (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=262) * debian/rules: Use autoreconf in lieu of automake&&autoconf&&... to avoid version skew. Thanks to James Westby for the patch. -- Nicholas Breen Mon, 19 Jan 2009 10:42:26 -0800 gromacs (4.0.2-1) unstable; urgency=low * New upstream release. - Remove obsoleted debian/patches/50_confio.dpatch (fixed), 10_manpages.dpatch (merged upstream). * debian/gromacs.README.Debian: suggest OpenMPI for new installations. -- Nicholas Breen Mon, 10 Nov 2008 12:36:15 -0800 gromacs (4.0-1) unstable; urgency=low * New upstream release. - debian/man: Remove g_nmtraj.1, g_sdf.1, g_spatial.1 (incorporated upstream). Remove average.1 (no longer shipped). Update gromacs.7 with changed commands and reference to new J. Chem. Theory Comput. paper. Update mdrun_mpi.*.1 based on upstream mdrun.1. Write new man pages xplor2gmx.1 and demux.1. - debian/lintian-overrides.gromacs: Update against new list of man pages. - debian/patches: Remove 05_autoconf_gsl.dpatch (fixed upstream) and 40_missing_cpp.dpatch (preprocessor functionality now built in). Resynchronize 10_manpages.dpatch. Add GROMACS 4 reference to 11_readme.dpatch. - debian/rules: Remove g_ffscan renaming (no longer shipped). * debian/control: Drop versioned dependency on base-files. Add Build- Depends on libtool. * debian/rules: Don't link MPI binaries to GSL, eliminating a spurious dependency. * patches/50_confio.dpatch: Avoid segfault when using make_ndx on .tpr files. (cf. http://www.gromacs.org/pipermail/gmx-developers/2008-October/002775.html) -- Nicholas Breen Wed, 29 Oct 2008 15:44:28 -0700 gromacs (3.3.3-3) unstable; urgency=low [ Daniel Leidert ] * debian/gromacs-data.doc-base (Section): Fixed accordingly to latest doc-base policy 0.8.10. [ Nicholas Breen ] * debian/README.source: add reference to dpatch system, as required by latest policy (sec. 4.14). Having done so: * debian/control: Update Standards-Version to 3.8.0. * debian/rules: Remove obsolete and now-inaccurate comment about parallel builds. Remove duplicated dh_installdeb call. * debian/man/g_kinetics.1: Update documentation. * debian/patches/05_autoconf_gsl.dpatch: libgsl was not properly detected by autoconf when the test didn't also link libgslcblas, rendering the g_kinetics program unusable. This changes the test to pass along LIBS appropriately. -- Nicholas Breen Wed, 20 Aug 2008 11:55:39 -0700 gromacs (3.3.3-2) unstable; urgency=low * debian/control: Eliminate unneeded Build-Depends on libxml-dev. Spotted by Pierre Habouzit. (Closes: #470000) * debian/rules: Force --with-gsl in configuration. -- Nicholas Breen Sat, 08 Mar 2008 12:34:36 -0800 gromacs (3.3.3-1) unstable; urgency=low [ Nicholas Breen ] * New upstream release. * debian/rules, debian/control: Reconfigure gromacs-doc as gromacs-data. This moves all architecture independent files into a single package, including many topology files formerly shipped in gromacs instead. - Rename debian/*gromacs-doc* to debian/*gromacs-data* . - debian/gromacs-doc.preinst: no longer necessary, removed. * Remove PDF manual for the time being, as modifiable sources are not currently available. - debian/gromacs.README.Debian, debian/man/gromacs.7: Provide pointers to its location online instead. - debian/control: Drop build dependency on sharutils, which was used only to provide the manual. - debian/gromacs-data.doc-base: Remove reference to PDF. * debian/control: Add Build-Depends on libgsl0-dev to support addition of /usr/bin/g_kinetics. * debian/gromacs.README.Debian: Update suggested MPI implementations. * debian/man: write preliminary man pages for undocumented new commands, g_kinetics.1 g_spatial.1 g_sdf.1 * debian/patches/10_manpages: Update with ROFF fixes to 18 files; fix a few minor typos; resync patch against upstream CVS. * debian/man/mdrun_mpi.{mpich,lam,openmpi}.1: Propagate those fixes. * debian/lintian-overrides.gromacs: Drop binary-without-manpage override. * debian/linda-overrides.gromacs, debian/rules: Remove linda override. [ Daniel Leidert ] * debian/man/average.1: Minor ROFF improvements, hyphen/minus and typo fixes. * debian/man/g_nmtraj.1: Ditto. * debian/man/luck.1: Ditto. -- Nicholas Breen Mon, 03 Mar 2008 21:23:01 -0800 gromacs (3.3.3~pre1-1) unstable; urgency=low [ Nicholas Breen ] * New upstream release. - Remove obsolete patches now incorporated upstream: 50_xtcio_double_range_checking, 51_180_degree_angle, 52_pme_spline, 53_pbc_compiler. * debian/rules: - Clean up patch syntax to prevent double compilations. - Add .NOTPARALLEL target to prevent the various MPI builds from compiling on the same source tree simultaneously, while still allowing -j options to be passed to sublevel targets. - Improve DEB_BUILD_OPTIONS=parallel=X handling, now in line with the example proposed for policy. - Disable FORTRAN inner loops for gromacs-openmpi on alpha. This is a temporary workaround to avoid lingering linking problems regarding libmpi.so and the update-alternatives system. - Add support for DEB_BUILD_OPTIONS=noopt. - Additional rewrite work (see below): use new format for build commands, but split for individual MPI implementations. - Run autotools between patch and configuration steps. - New format for MPI library suffix configuration. * debian/control: - Add versioned Build-Depends on libmpich1.0-dev for its g77 -> gfortran transition. - Add Build-Depends on autoconf and automake, and Build-Conflicts on autoconf2.13, to support updated mpisuffix patch. - Downgrade gromacs-doc Depends: on gromacs to a Recommends:, as -doc now ships its own copyright file. * debian/patches/04_autoconf_mpisuffix.dpatch: Apply dleidert's improved patch to allow arbitrary overrides of LIBSUFFIX; reduce patch to only the directly changed code in configure.ac, and add an invocation of autotools during the build process rather than patching configure itself directly. * debian/gromacs-{doc,dev}.preinst: Remove symlinks for package doc directories on upgrade, in order to replace them with actual directories. [ Daniel Leidert ] * debian/control (Suggests): Fixed a debcheck issue - gromacs-openmpi should only be suggested on supported architectures. * debian/copyright: Added copyright information to satisfy lintian. * debian/gromacs-doc.doc-base (Section): Fixed accordingly to menu policy. (Format): Fixed path to HTML files. * debian/rules: Major rewrite. Changes/improvements include: - drop dpatch target definitions in favour of dpatch.make - put all configure flags to the top of the file - moved all configure related commands into configure-stamp - moved all build related commands into build-stamp - moved all install related commands into separate install targets - configure and build in sub-directories to avoid $(MAKE) clean calls - clean target removes build/ instead to run clean/distclean - replaced ln with dh_link and gzip with dh_installman - adjusted target requirements for binary* and install* - install a /usr/share/doc/$package directory for gromacs-doc and -dev too; put the HTML into the -doc documentation directory; add links to the HTML directory for the gromacs and the -dev package pointing to the -doc directory - fixed .PHONY target for above * debian/watch: Added pre-release version handling. -- Nicholas Breen Wed, 13 Feb 2008 15:01:50 -0800 gromacs (3.3.2-3) unstable; urgency=low * Package transferred to Debichem team maintenance. * debian/control: - Switched Maintainer to Debichem Team, moved myself to Uploaders. Added Vcs-Browser, Vcs-Svn fields. - Increase Standards-Version to 3.7.3. No changes required. - Build-Depend on libopenmpi-dev >= 1.2.4-5 (Closes: #456860). * debian/rules: include kfreebsd-* variants explicitly in OPENMPI_ARCH. * debian/patches/11_readme.dpatch: change edited README to an explicit patch, rather than modifying it directly in the .diff.gz. * Multiple bugfixes from upstream CVS: - 51_180_degree_angle.dpatch: apply upstream patches to avoid crashes crashes when operating on precisely linear 2-bond pairs. (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=172, http://bugzilla.gromacs.org/show_bug.cgi?id=177) - 52_pme_spline.dpatch: calculate mesh contribution when charges are 0 in A state, but non-zero in B state. (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=175) - 53_pbc_compiler: Solve regression in gmxlib/pbc.c introduced by a previous compiler workaround. (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=179) * debian/gromacs-doc.doc-base: remove extraneous spaces. -- Nicholas Breen Wed, 26 Dec 2007 12:26:09 -0800 gromacs (3.3.2-2) unstable; urgency=low * Add support for OpenMPI with new "gromacs-openmpi" binary package. Thanks to Manuel Prinz for assistance. (Closes: #448635) * Build binaries for double-precision floating point operations, in addition to the existing single-precision binaries. Double precision commands are denoted by a "_d" suffix. * debian/control: Update feature summary URL in package description, and add Homepage field. * Reformat all man page headers to work with whatis(1), apropos(1), and similar tools. -- Nicholas Breen Tue, 13 Nov 2007 13:03:22 -0800 gromacs (3.3.2-1) unstable; urgency=low * New upstream release. (Closes: #446760) - Incorporates fix for amd64 double-precision builds. (Closes: #442886) - Remove obsolete patches 50_gmx_order, 51_libxdrf_trajectory, 52_genion_compiler_workaround, 60_amd64_double. * Add a Recommends: cpp to gromacs binary package, and improve the error message given by grompp when no preprocessor is installed to clarify the "-pp" option. (Closes: #442139) * Update Build-Depends to reflect fftw3-dev -> libfftw3-dev renaming. * Conflict with radiance (<= 3R8+20070924.dfsg-1) due to overlapping /usr/bin/genbox. Related to #446726, which will be closed by a future upload of radiance. * src/gmxlib/xtcio.c: import upstream fix for range checking failures when running both parallel and double-precision simulations. (cf. http://www.gromacs.org/pipermail/gmx-users/2007-October/029990.html) -- Nicholas Breen Mon, 15 Oct 2007 14:39:30 -0700 gromacs (3.3.1-7) unstable; urgency=low * debian/rules: correct typo that broke alpha builds. -- Nicholas Breen Tue, 11 Sep 2007 12:23:52 -0700 gromacs (3.3.1-6) unstable; urgency=low * Update alpha Build-Depends from g77 to gfortran, and set F77 variable in debian/rules accordingly. * Increase update-alternatives priority of mdrun_mpi.lam to 20. * src/tools/gmx_xpm2ps.c: explicitly initialize 'ninp' to 0 to work around a peculiar compiler/shared-library/i386 bug. (Closes: #428795) * debian/copyright: clarify license as GPL v2 or later. Add Depends: on base-files (>=4.0.1) until the next release to ensure that the GPL v3 license text is installed as well. (Closes: #435208) * When building from source, two DEB_BUILD_OPTIONS are available: - "parallel" adds -j4 to the make flags. - "double" will compile binaries for both single-precision (the default) and double-precision (with _d suffix) floating point operations. * Minor packaging cleanups: set debhelper compatibility level to 5, clarify versioned dependencies for -doc and -dev packages, improve "make clean" error handling, clean up lintian overrides. -- Nicholas Breen Mon, 10 Sep 2007 17:29:10 -0700 gromacs (3.3.1-5) unstable; urgency=low * Workaround for compiler problems on some platforms that could cause genion to hang in an infinite loop when using cubic boxes. (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=108) * Eliminate spurious mdrun warnings when using triclinic boxes. (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=121) -- Nicholas Breen Tue, 10 Apr 2007 17:08:02 -0700 gromacs (3.3.1-4) unstable; urgency=medium * Rename /usr/bin/ffscan to g_ffscan, resolving a filename conflict with the 'forutil' package. (Closes: #403879) -- Nicholas Breen Sat, 23 Dec 2006 11:24:59 -0800 gromacs (3.3.1-3) unstable; urgency=low * Update URL to features list in package description. (Closes: #393750) * Correct deuterium order parameter generation in src/tools/g_order.c. (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=84) * Patch src/gmxlib/libxdrf.c to eliminate errors when the specified time for a search inside a trajectory falls on a frame boundary. (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=106) -- Nicholas Breen Wed, 6 Dec 2006 11:04:01 -0800 gromacs (3.3.1-2) unstable; urgency=low * _Really_ register gromacs-doc with doc-base. (The previous attempt contained an error.) Thanks again to Drew Parsons. (Closes: #359999) * Update Standards-Version to 3.7.2. No packaging changes required. -- Nicholas Breen Tue, 26 Sep 2006 15:21:48 -0700 gromacs (3.3.1-1) unstable; urgency=low * New upstream release. * Updated PDF manual to 3.3 release. * disco(1) is no longer shipped, so it no longer needs renaming. -- Nicholas Breen Thu, 13 Apr 2006 15:53:29 -0700 gromacs (3.3-2) unstable; urgency=low * Adding Build-Depends on g77 for alpha only. (No other architectures use FORTRAN inner loops by default.) (Closes: #360486) * Recategorizing to different parts of archive: gromacs-doc to 'doc', gromacs-dev to 'devel'. * Correct implicit pointer size declaration in src/mdlib/ghat.c, which could lead to segfaults on 64-bit architectures. Thanks to Dann Frazier for catching it. (Closes: #360002) * Registered gromacs-doc with doc-base. Patch courtesy of Drew Parsons. (Closes: #359999) * Renaming /usr/bin/disco to g_disco, to avoid filename conflict with mono-mcs. (Closes: #360374) -- Nicholas Breen Mon, 3 Apr 2006 09:50:44 -0700 gromacs (3.3-1) unstable; urgency=low * Initial Debian release. (Closes: #228319, #252101) -- Nicholas Breen Thu, 16 Mar 2006 23:00:13 -0800 debian/upstream0000664000000000000000000000240512065651577010772 0ustar Name: GROMACS Reference: - Author: Berk Hess and Carsten Kutzner and David van der Spoel and Erik Lindahl Title: "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation" Journal: J. Chem. Theory Comput. Year: 2008 Volume: 4 Number: 3 Pages: 435-447 URL: http://pubs.acs.org/doi/abs/10.1021/ct700301q eprint: http://pubs.acs.org/doi/pdfplus/10.1021/ct700301q DOI: 10.1021/ct700301q - Author: Erik Lindahl and Berk Hess and David van der Spoel Title: "GROMACS 3.0: A Package for Molecular Simulation and Trajectory Analysis" Journal: J Mol Model. Year: 2001 Volume: 7 Number: 8 Pages: 306-17 DOI: 10.1007/s008940100045 URL: http://www.springerlink.com/content/r894b1jx35la6eja/ eprint: http://www.springerlink.com/content/r894b1jx35la6eja/fulltext.pdf - Author: David van der Spoel and Erik Lindahl and Berk Hess and Gerrit Groenhof and Alan E. Mark and Herman J. C. Berendsen Title: "GROMACS: Fast, Flexible, and Free" Journal: J Comput Chem. Year: 2005 Volume: 26 Number: 16 Pages: 1701-18 PMID: 16211538 DOI: 10.1002/jcc.20291 URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20291/abstract eprint: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20291/pdf debian/gromacs-mpich.prerm0000664000000000000000000000051111011457627012771 0ustar #! /bin/sh # prerm script for gromacs-mpich set -e case "$1" in upgrade) ;; remove|deconfigure|failed-upgrade) update-alternatives --remove mdrun_mpi /usr/bin/mdrun_mpi.mpich ;; *) echo "prerm called with unknown argument \`$1'" >&2 exit 1 ;; esac #DEBHELPER# exit 0 debian/compat0000664000000000000000000000000211310620171010356 0ustar 7 debian/gromacs-parallel.README.Debian.in0000664000000000000000000000264511361260352015070 0ustar gromacs with #MPIPROG# support for Debian ----------------------------------------------------------------------- This package contains the MPI-enabled version of the GROMACS molecular dynamics engine, compiled for use with #MPIPROG#. The binary is named "mdrun_mpi.#MPIABBR#", though it is aliased to "mdrun_mpi". For non-MPI applications, use the single-threaded "mdrun" in the gromacs package. Versions of mdrun_mpi compiled for OpenMPI and MPICH can be installed in parallel. In this case, the OpenMPI build will take priority as the default version (the one that controls the mdrun_mpi alias) -- you may change this with update-alternatives(8). One minor consequence of this design is that third-party applications that link to the GROMACS MPI-enabled shared libraries will not work without setting up compatibility symlinks, nor will such binaries compiled on Debian systems work elsewhere. I am not currently aware of any such applications, but in case you've got any, here's what you need to know: * /usr/lib/libgmx_mpi.so has been renamed to libgmx_mpi_#MPIABBR#.so * /usr/lib/libmd_mpi.so has been renamed to libmd_mpi_#MPIABBR#.so * The library SONAMEs have changed accordingly * The same transformations have been applied to the static libraries (.a extensions) * The non-MPI libraries in the gromacs and gromacs-dev packages are unaffected. -- Nicholas Breen , Fri, 21 Oct 2005 11:27:27 -0400 debian/gromacs.dirs0000664000000000000000000000005011635734227011513 0ustar usr/share/gromacs usr/share/doc/gromacs debian/gromacs-data.dirs0000664000000000000000000000017611635734227012433 0ustar usr/share/doc/gromacs usr/share/doc/gromacs-data usr/share/doc/gromacs-dev usr/share/gromacs usr/share/gromacs/shell-specific debian/copyright0000664000000000000000000000344411310620171011120 0ustar This Debian-packaged version of GROMACS was assembled by Nicholas Breen from the original sources at http://www.gromacs.org/ . There have been a number of key GROMACS developers across its history. The current developers are: * David van der Spoel * Berk Hess * Erik Lindahl Former contributors include: * Emile Apol * Henk Bekker * Herman Berendsen * Aldert van Buuren * Rudi van Drunen * Anton Feenstra * Bert de Groot * Pieter Meulenhoff * Alfons Sijbers * Peter Tieleman Copyright: Copyright (c) 1991-2001, University of Groningen, The Netherlands. Copyright (c) 2001-2009, The GROMACS development team. License: This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA On Debian systems, the complete text of the GNU General Public License can be found in `/usr/share/common-licenses/GPL'. Version 2 of the GPL is in `/usr/share/common-licenses/GPL-2'. The Debian packaging is copyright (C) 2005-2009 Nicholas Breen and the Debichem Team, and is licensed under the GPL v.2 or later, as above. debian/source/0000775000000000000000000000000012251262734010474 5ustar debian/source/format0000664000000000000000000000001411755335355011712 0ustar 3.0 (quilt) debian/source/lintian-overrides0000664000000000000000000000043512251262734014057 0ustar gromacs source: debhelper-but-no-misc-depends gromacs-data # http://bugs.debian.org/724866 gromacs source: virtual-package-depends-without-real-package-depends build-depends: libmpich-dev # http://bugs.debian.org/729096 gromacs source: newer-standards-version 3.9.5 (current is 3.9.4) debian/gromacs-mpich.postinst0000664000000000000000000000320211011457627013527 0ustar #! /bin/sh # postinst script for gromacs-mpich # # see: dh_installdeb(1) set -e # summary of how this script can be called: # * `configure' # * `abort-upgrade' # * `abort-remove' `in-favour' # # * `abort-deconfigure' `in-favour' # `removing' # # for details, see http://www.debian.org/doc/debian-policy/ or # the debian-policy package # # quoting from the policy: # Any necessary prompting should almost always be confined to the # post-installation script, and should be protected with a conditional # so that unnecessary prompting doesn't happen if a package's # installation fails and the `postinst' is called with `abort-upgrade', # `abort-remove' or `abort-deconfigure'. case "$1" in configure) update-alternatives \ --install /usr/bin/mdrun_mpi mdrun_mpi /usr/bin/mdrun_mpi.mpich 10 \ --slave /usr/bin/mdrun_mpi_d mdrun_mpi_d /usr/bin/mdrun_mpi_d.mpich \ --slave /usr/share/man/man1/mdrun_mpi.1.gz mdrun_mpi.1.gz /usr/share/man/man1/mdrun_mpi.mpich.1.gz \ --slave /usr/share/man/man1/mdrun_mpi_d.1.gz mdrun_mpi_d.1.gz /usr/share/man/man1/mdrun_mpi_d.mpich.1.gz ;; abort-upgrade|abort-remove|abort-deconfigure) ;; *) echo "postinst called with unknown argument \`$1'" >&2 exit 1 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0 debian/gromacs-openmpi.prerm0000664000000000000000000000051511011457627013344 0ustar #! /bin/sh # prerm script for gromacs-openmpi set -e case "$1" in upgrade) ;; remove|deconfigure|failed-upgrade) update-alternatives --remove mdrun_mpi /usr/bin/mdrun_mpi.openmpi ;; *) echo "prerm called with unknown argument \`$1'" >&2 exit 1 ;; esac #DEBHELPER# exit 0 debian/gromacs-openmpi.dirs0000664000000000000000000000006711011457627013162 0ustar usr/bin usr/share/man/man1 usr/share/lintian/overrides debian/gromacs-openmpi.postinst0000664000000000000000000000326111124354443014100 0ustar #! /bin/sh # postinst script for gromacs-openmpi # # see: dh_installdeb(1) set -e # summary of how this script can be called: # * `configure' # * `abort-upgrade' # * `abort-remove' `in-favour' # # * `abort-deconfigure' `in-favour' # `removing' # # for details, see http://www.debian.org/doc/debian-policy/ or # the debian-policy package # # quoting from the policy: # Any necessary prompting should almost always be confined to the # post-installation script, and should be protected with a conditional # so that unnecessary prompting doesn't happen if a package's # installation fails and the `postinst' is called with `abort-upgrade', # `abort-remove' or `abort-deconfigure'. case "$1" in configure) update-alternatives \ --install /usr/bin/mdrun_mpi mdrun_mpi /usr/bin/mdrun_mpi.openmpi 25 \ --slave /usr/bin/mdrun_mpi_d mdrun_mpi_d /usr/bin/mdrun_mpi_d.openmpi \ --slave /usr/share/man/man1/mdrun_mpi.1.gz mdrun_mpi.1.gz /usr/share/man/man1/mdrun_mpi.openmpi.1.gz \ --slave /usr/share/man/man1/mdrun_mpi_d.1.gz mdrun_mpi_d.1.gz /usr/share/man/man1/mdrun_mpi_d.openmpi.1.gz ;; abort-upgrade|abort-remove|abort-deconfigure) ;; *) echo "postinst called with unknown argument \`$1'" >&2 exit 1 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. # Specifically, the 'ldconfig' call. #DEBHELPER# exit 0 debian/gromacs-data.doc-base0000664000000000000000000000062412251430422013126 0ustar Document: gromacs Title: Gromacs Manual Author: David van der Spoel and others Abstract: This manual describes the configuration and use of gromacs, a program designed to perform molecular dynamics simulations extremely quickly. Section: Science/Chemistry Format: HTML Index: /usr/share/doc/gromacs/html/online/getting_started.html Files: /usr/share/doc/gromacs/html/online/*.html debian/gromacs-mpich.lintian-overrides0000664000000000000000000000133012201767060015277 0ustar gromacs-mpich: package-name-doesnt-match-sonames # Adaptive Resolution Molecular Dynamics Simulation gromacs-mpich: spelling-error-in-binary usr/lib/libgmxpreprocess_mpi.mpich.so.8 AdResS Address gromacs-mpich: spelling-error-in-binary usr/lib/libgmxpreprocess_mpi_d.mpich.so.8 AdResS Address gromacs-mpich: spelling-error-in-binary usr/lib/libmd_mpi.mpich.so.8 AdResS Address gromacs-mpich: spelling-error-in-binary usr/lib/libmd_mpi_d.mpich.so.8 AdResS Address gromacs-mpich: spelling-error-in-binary usr/lib/libgmx_mpi.mpich.so.8 AdResS Address gromacs-mpich: spelling-error-in-binary usr/lib/libgmx_mpi_d.mpich.so.8 AdResS Address # too small to merit a -dev package of its own gromacs-mpich: non-dev-pkg-with-shlib-symlink debian/gromacs.lintian-overrides0000664000000000000000000000137412201767060014211 0ustar # no need to split out the libraries into separate lib packages, # since no other package uses them gromacs: package-name-doesnt-match-sonames # Adaptive Resolution Molecular Dynamics Simulation gromacs: spelling-error-in-binary usr/bin/grompp AdResS Address gromacs: spelling-error-in-binary usr/bin/grompp_d AdResS Address gromacs: spelling-error-in-binary usr/lib/libgmxpreprocess.so.8 AdResS Address gromacs: spelling-error-in-binary usr/lib/libgmxpreprocess_d.so.8 AdResS Address gromacs: spelling-error-in-binary usr/lib/libmd.so.8 AdResS Address gromacs: spelling-error-in-binary usr/lib/libmd_d.so.8 AdResS Address gromacs: spelling-error-in-binary usr/lib/libgmx.so.8 AdResS Address gromacs: spelling-error-in-binary usr/lib/libgmx_d.so.8 AdResS Address debian/control0000664000000000000000000001306212250743576010610 0ustar Source: gromacs Section: science Priority: extra Maintainer: Debichem Team Uploaders: Nicholas Breen Build-Depends: debhelper (>= 7.0.0), libfftw3-dev, libmpich-dev (>= 3), libopenmpi-dev (>= 1.2.4-5) [alpha amd64 armel armhf i386 ia64 powerpc powerpcspe ppc64 sparc sparc64 kfreebsd-i386 kfreebsd-amd64 hurd-i386], libx11-dev, zlib1g-dev, libgsl0-dev, libxml2-dev, libblas-dev, liblapack-dev, cmake, hardening-wrapper, chrpath Standards-Version: 3.9.5 Homepage: http://www.gromacs.org/ Vcs-Browser: http://anonscm.debian.org/viewvc/debichem/ Vcs-Svn: svn://anonscm.debian.org/debichem/unstable/gromacs/ Package: gromacs Architecture: any Depends: gromacs-data (= ${source:Version}), ${shlibs:Depends}, ${misc:Depends} Recommends: cpp Suggests: pymol Description: Molecular dynamics simulator, with building and analysis tools GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. . It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers. . GROMACS offers entirely too many features for a brief description to do it justice. A more complete listing is available at . Package: gromacs-data Architecture: all Recommends: gromacs Suggests: tcsh | c-shell Conflicts: gromacs-doc Breaks: gromacs (<< 3.3.3-1) Replaces: gromacs-doc Description: GROMACS molecular dynamics sim, data and documentation GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. . It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers. . This package contains architecture-independent topology and force field data, documentation, man pages, and example files. Package: gromacs-dev Architecture: any Section: devel Depends: ${shlibs:Depends}, gromacs (= ${binary:Version}), fftw3-dev, ${misc:Depends} Recommends: gromacs-data Suggests: gromacs-mpich (= ${binary:Version}) | gromacs-openmpi (= ${binary:Version}) [alpha amd64 armel armhf i386 ia64 powerpc powerpcspe sparc sparc64 kfreebsd-i386 kfreebsd-amd64 hurd-i386], libmpich-dev, libx11-dev, zlib1g-dev Description: GROMACS molecular dynamics sim, development kit GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. . It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers. . This package contains header files and static libraries for development purposes, plus sample Makefiles. Development components for MPI-enabled GROMACS builds also require their respective packages. Package: gromacs-mpich Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, mpich Recommends: gromacs Suggests: gromacs-data Replaces: gromacs-dev (<< 4.6.3-3~) Breaks: gromacs-dev (<< 4.6.3-3~) Description: Molecular dynamics sim, binaries for MPICH parallelization GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. . It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers. . This package contains only the core simulation engine with parallel support using the MPICH (v3) interface. It is suitable for nodes of a processing cluster, or for multiprocessor machines. Package: gromacs-openmpi Architecture: alpha amd64 armel armhf i386 ia64 powerpc powerpcspe ppc64 sparc sparc64 kfreebsd-i386 kfreebsd-amd64 hurd-i386 Depends: ${shlibs:Depends}, ${misc:Depends}, openmpi-bin (>= 1.2.3) Recommends: gromacs Suggests: gromacs-data Replaces: gromacs-lam, gromacs-dev (<< 4.6.3-3~) Breaks: gromacs-dev (<< 4.6.3-3~) Description: Molecular dynamics sim, binaries for OpenMPI parallelization GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. . It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non- biological systems, e.g. polymers. . This package contains only the core simulation engine with parallel support using the OpenMPI interface. It is suitable for nodes of a processing cluster, or for multiprocessor machines. debian/docs0000664000000000000000000000001711011457627010045 0ustar README AUTHORS debian/gromacs-data.lintian-overrides0000664000000000000000000000006512122132530015102 0ustar # demo scripts # gromacs-data: script-not-executable debian/gromacs-mpich.dirs0000664000000000000000000000003311635734227012612 0ustar usr/bin usr/share/man/man1 debian/patches/0000775000000000000000000000000012251423540010615 5ustar debian/patches/20_manpages.patch0000664000000000000000000002146312251423540013740 0ustar Description: Fix formatting errors in NAME lines Author: Nicholas Breen Origin: vendor Index: gromacs-4.6.5/man/man1/do_dssp.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/do_dssp.1 2013-12-02 14:06:09.000000000 -0800 +++ gromacs-4.6.5/man/man1/do_dssp.1 2013-12-08 22:45:23.971449475 -0800 @@ -1,6 +1,6 @@ .TH do_dssp 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -do_dssp\ -\ assigns\ secondary\ structure\ and\ calculates\ solvent\ accessible\ surface\ area +do_dssp \- assigns secondary structure and calculates solvent accessible surface area .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/g_angle.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/g_angle.1 2013-12-02 14:06:09.000000000 -0800 +++ gromacs-4.6.5/man/man1/g_angle.1 2013-12-08 22:45:32.587456179 -0800 @@ -1,6 +1,6 @@ .TH g_angle 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -g_angle\ -\ calculates\ distributions\ and\ correlations\ for\ angles\ and\ dihedrals +g_angle \- calculates distributions and correlations for angles and dihedrals .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/g_bar.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/g_bar.1 2013-12-02 14:06:09.000000000 -0800 +++ gromacs-4.6.5/man/man1/g_bar.1 2013-12-08 22:46:02.543479453 -0800 @@ -1,6 +1,6 @@ .TH g_bar 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -g_bar\ -\ calculates\ free\ energy\ difference\ estimates\ through\ Bennett's\ acceptance\ ratio +g_bar \- calculates free energy difference estimates through Bennett's acceptance ratio .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/g_chi.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/g_chi.1 2013-12-02 14:06:09.000000000 -0800 +++ gromacs-4.6.5/man/man1/g_chi.1 2013-12-08 22:46:16.911490055 -0800 @@ -1,6 +1,6 @@ .TH g_chi 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -g_chi\ -\ calculates\ everything\ you\ want\ to\ know\ about\ chi\ and\ other\ dihedrals +g_chi \- calculates everything you want to know about chi and other dihedrals .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/g_filter.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/g_filter.1 2013-12-02 14:06:09.000000000 -0800 +++ gromacs-4.6.5/man/man1/g_filter.1 2013-12-08 22:46:23.971493543 -0800 @@ -1,6 +1,6 @@ .TH g_filter 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -g_filter\ -\ frequency\ filters\ trajectories,\ useful\ for\ making\ smooth\ movies +g_filter \- frequency filters trajectories, useful for making smooth movies .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/g_helixorient.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/g_helixorient.1 2013-12-02 14:06:09.000000000 -0800 +++ gromacs-4.6.5/man/man1/g_helixorient.1 2013-12-08 22:46:31.951497491 -0800 @@ -1,6 +1,6 @@ .TH g_helixorient 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -g_helixorient\ -\ calculates\ local\ pitch/bending/rotation/orientation\ inside\ helices +g_helixorient \- calculates local pitch/bending/rotation/orientation inside helices .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/g_rmsdist.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/g_rmsdist.1 2013-12-02 14:06:10.000000000 -0800 +++ gromacs-4.6.5/man/man1/g_rmsdist.1 2013-12-09 12:26:06.620833029 -0800 @@ -1,6 +1,6 @@ .TH g_rmsdist 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -g_rmsdist\ -\ calculates\ atom\ pair\ distances\ averaged\ with\ power\ -2,\ -3\ or\ -6 +g_rmsdist \- calculates atom pair distances averaged with power \-2, \-3 or \-6 .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/g_rotmat.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/g_rotmat.1 2013-12-02 14:06:10.000000000 -0800 +++ gromacs-4.6.5/man/man1/g_rotmat.1 2013-12-08 22:46:45.067503977 -0800 @@ -1,6 +1,6 @@ .TH g_rotmat 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -g_rotmat\ -\ plots\ the\ rotation\ matrix\ for\ fitting\ to\ a\ reference\ structure +g_rotmat \- plots the rotation matrix for fitting to a reference structure .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/g_sigeps.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/g_sigeps.1 2013-12-02 14:06:10.000000000 -0800 +++ gromacs-4.6.5/man/man1/g_sigeps.1 2013-12-08 22:46:51.775507295 -0800 @@ -1,6 +1,6 @@ .TH g_sigeps 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -g_sigeps\ -\ convert\ c6/12\ or\ c6/cn\ combinations\ to\ and\ from\ sigma/epsilon +g_sigeps \- convert c6/12 or c6/cn combinations to and from sigma/epsilon .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/g_spol.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/g_spol.1 2013-12-02 14:06:10.000000000 -0800 +++ gromacs-4.6.5/man/man1/g_spol.1 2013-12-08 22:46:57.407510081 -0800 @@ -1,6 +1,6 @@ .TH g_spol 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -g_spol\ -\ analyzes\ solvent\ dipole\ orientation\ and\ polarization\ around\ solutes +g_spol \- analyzes solvent dipole orientation and polarization around solutes .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/g_traj.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/g_traj.1 2013-12-02 14:06:10.000000000 -0800 +++ gromacs-4.6.5/man/man1/g_traj.1 2013-12-08 22:47:03.875513279 -0800 @@ -1,6 +1,6 @@ .TH g_traj 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -g_traj\ -\ plots\ x,\ v\ and\ f\ of\ selected\ atoms/groups\ (and\ more)\ from\ a\ trajectory +g_traj \- plots x, v and f of selected atoms/groups (and more) from a trajectory .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/genion.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/genion.1 2013-12-02 14:06:10.000000000 -0800 +++ gromacs-4.6.5/man/man1/genion.1 2013-12-08 22:47:09.991516306 -0800 @@ -1,6 +1,6 @@ .TH genion 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -genion\ -\ generates\ mono\ atomic\ ions\ on\ energetically\ favorable\ positions +genion \- generates mono atomic ions on energetically favorable positions .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/genrestr.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/genrestr.1 2013-12-02 14:06:10.000000000 -0800 +++ gromacs-4.6.5/man/man1/genrestr.1 2013-12-08 22:47:18.663520596 -0800 @@ -1,6 +1,6 @@ .TH genrestr 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -genrestr\ -\ generates\ position\ restraints\ or\ distance\ restraints\ for\ index\ groups +genrestr \- generates position restraints or distance restraints for index groups .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/mdrun.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/mdrun.1 2013-12-02 14:06:08.000000000 -0800 +++ gromacs-4.6.5/man/man1/mdrun.1 2013-12-08 22:47:24.039523256 -0800 @@ -1,6 +1,6 @@ .TH mdrun 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -mdrun\ -\ performs\ a\ simulation,\ do\ a\ normal\ mode\ analysis\ or\ an\ energy\ minimization +mdrun \- performs a simulation, do a normal mode analysis or an energy minimization .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/pdb2gmx.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/pdb2gmx.1 2013-12-02 14:06:07.000000000 -0800 +++ gromacs-4.6.5/man/man1/pdb2gmx.1 2013-12-08 22:47:32.239527316 -0800 @@ -1,6 +1,6 @@ .TH pdb2gmx 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -pdb2gmx\ -\ converts\ coordinate\ files\ to\ topology\ and\ FF-compliant\ coordinate\ files +pdb2gmx \- converts coordinate files to topology and FF-compliant coordinate files .B VERSION 4.6.5 .SH SYNOPSIS Index: gromacs-4.6.5/man/man1/g_dist.1 =================================================================== --- gromacs-4.6.5.orig/man/man1/g_dist.1 2013-12-02 14:06:09.000000000 -0800 +++ gromacs-4.6.5/man/man1/g_dist.1 2013-12-08 23:02:49.799984554 -0800 @@ -1,6 +1,6 @@ .TH g_dist 1 "Mon 2 Dec 2013" "" "GROMACS suite, VERSION 4.6.5" .SH NAME -g_dist\ -\ calculates\ the\ distances\ between\ the\ centers\ of\ mass\ of\ two\ groups +g_dist \- calculates the distances between the centers of mass of two groups .B VERSION 4.6.5 .SH SYNOPSIS debian/patches/12_copyright-file.patch0000664000000000000000000000252012144776346015104 0ustar Description: Install only a single copyright file Avoid duplication of COPYING and debian/copyright. A symlink is provided between the two. Author: Nicholas Breen Origin: vendor Forwarded: not-needed Last-Update: 2013-05-15 --- Index: gromacs-4.6.1/CMakeLists.txt =================================================================== --- gromacs-4.6.1.orig/CMakeLists.txt 2013-05-15 14:23:46.068432259 -0700 +++ gromacs-4.6.1/CMakeLists.txt 2013-05-15 14:23:46.068432259 -0700 @@ -113,7 +113,7 @@ endif() set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt") # Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this... -set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING") +set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/debian/copyright") set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt") set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$") set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake") @@ -1123,7 +1123,7 @@ #COPYING file: Only necessary for binary distributions. #Simpler to always install. -install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data) +install(FILES DESTINATION ${DATA_INSTALL_DIR} COMPONENT data) add_subdirectory(share) add_subdirectory(include) debian/patches/series0000664000000000000000000000007212251263141012030 0ustar 11_readme.patch 12_copyright-file.patch 20_manpages.patch debian/patches/11_readme.patch0000664000000000000000000000247512144776273013423 0ustar Description: Edit README to explain that this is not an official upstream build Origin: vendor Author: Nicholas Breen Index: gromacs-4.6.1/README =================================================================== --- gromacs-4.6.1.orig/README 2013-05-15 14:22:01.468187072 -0700 +++ gromacs-4.6.1/README 2013-05-15 14:23:05.264336300 -0700 @@ -1,5 +1,5 @@ - Welcome to the official version of GROMACS! + Welcome to the Debian version of GROMACS! If you are familiar with Unix, it should be fairly trivial to compile and install GROMACS. GROMACS uses only the CMake build sytem, and our @@ -40,6 +40,12 @@ sure support questions are directed to you instead of the GROMACS developers. Sorry for the hard wording, but it is meant to protect YOUR reseach results! ++----------------------------------------------------------------------------+ +| Debian users: that means the Bug Tracking System, http://bugs.debian.org/ | +| (Although this IS technically a derived version, no significant changes | +| have been made to the upstream code -- it should behave identically.) | ++----------------------------------------------------------------------------+ + * * * * * The development of GROMACS is mainly funded by academic research grants. debian/gromacs-dev.preinst0000664000000000000000000000172311011457627013014 0ustar #!/bin/sh # preinst script for gromacs-dev # # see: dh_installdeb(1) set -e # summary of how this script can be called: # * `install' # * `install' # * `upgrade' # * `abort-upgrade' # for details, see http://www.debian.org/doc/debian-policy/ or # the debian-policy package case "$1" in upgrade) # versions prior to 3.3.3~pre1-1 shipped /usr/share/doc/gromacs-dev as a # symlink; this must be removed before installing newer versions that # ship it as a directory instead. if [ -L /usr/share/doc/gromacs-dev ] ; then rm -f /usr/share/doc/gromacs-dev fi ;; install|abort-upgrade) ;; *) echo "preinst called with unknown argument \`$1'" >&2 exit 1 ;; esac # dh_installdeb will replace this with shell code automatically # generated by other debhelper scripts. #DEBHELPER# exit 0