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Update to GROMACS 4.5.1

Browse source 
GROMACS 4.5.1 is bug fix release.


Release notes for 4.5

New features

  * Pencil decomposition of the reciprocal space PME grid to
    improve scaling. This reduces the amount of communication
    for high parallelization and improves load balancing with up
    to 40% overall performance improvement for large systems.
  * Memory usage is improved for very large systems, allowing
    simulations of >100 million atoms.
  * Running on a multi-core node now uses thread-based
    parallelization to automatically spawn the optimum number of
    threads in the default build. MPI is now only required for
    parallelization over the network.
  * Domain decomposition can now also be used without periodic
    boundary conditions
  * GPU acceleration support on NVIDIA cards. This first release
    with GPU support based on OpenMM provides up to an order of
    magnitude faster performance for implicit solvent simulations,
    but PME simulations are about as fast as on a high-end CPU.
  * Check-pointing is made more secure:MD5sum are used to verify
    that all files are correctly in-place before a simulation is
    appended. Output file appending at continuation is turned on
    by default.
  * Increased tolerance for networked file system failures and
    cluster node crashes: checkpoint handling is safer and mdrun
    forces file system cache flushes during checkpoints.
  * Full CMake support. After the 4.5 release we will be
    switching the default build tool from autoconf to cmake,
    and possibly deprecate autoconf in the future.
  * Full support for seven AMBER force fields in the standard
    distribution, with default Amber names. We also include the
    recent Amber99sb-ildn in the distribution.
  * Support for CHARMM27, including cmap for dihedrals
  * Efficient Generalized-Born implicit solvent support
    including the Still/HCT/OBC-models to compute the Born radii,
    a novel way of tabulating the generalized Born-interaction
    formula for greater speed, and optimized SSE-routines in both
    single and double precision.
  * Highly efficient all-vs-all assembly kernels for both vanilla
    and generalized born interactions, in both single and double
    precision.
  * Much better support for nucleic acid simulations, including
    automatic handling by pdb2gmx.
  * Support for Velocity-Verlet integrators for reversible T-
    and P-coupling; MTTK pressure control integrators;
    Nose-Hoover chains.
  * Symplectic Trotter Leap-Frog integrator for twin-range
    non-bonded interactions.
  * Support for Bennet acceptance ratio calculations through
    direct calculation of Hamiltonian differences during the
    simulation.
  * File formats: All GROMACS tools can now read any VMD
    supported trajectory format, without converting trajectory
    first. (VMD libraries are required).
  * pdb2gmx now retains the residue numbers from the input,
    mdrun and all tools use these original numbers.

New tools

  * g_bar: Bennett acceptance ratio (BAR) free energy calculations,
    including automatic error estimates and phase space overlap
    measures.
  * g_rdf was a little bit enhanced that structure factors can
    be calculated for any system, by supplying the necessary data
    via sfactor.dat. Most of the common atomtypes are already
    contained, but everybody who needs more freedom can enhance
    the table
  * g_select: Library support for "dynamic index groups" based
    on textual selections (experimental feature).
    See the tool g_select, the included template.c, or Doxygen
    documentation for information on how to write analysis tools
    using the library. Existing tools have not (yet) been
    converted.
  * g_tune_pme: For a given number of processes or threads this
    tool systematically times mdrun with various numbers of
    PME-only nodes and determines which setting is fastest. It
    also checks whether performance can be enhanced by shifting
    load between the real and the reciprocal space part of the
    Ewald sum.
  * g_membed: a very convenient utility for rapidly embedding
    membrane proteins into equilibrated lipid bilayers
  * g_pme_error: estimates the error of the electrostatic forces
    if using the SPME algorithm. TO be incorporated in g_tune_pme

Changes that might affect your results

  * grompp by default sets the new nstcalcenergy parameter equal
    to nstlist, this has no effect on the integration, only on
    the energy averages stored in ener.edr
  * grompp by default sets the new nsttcouple parameter equal to
    nstlist, this means T-coupling is done less frequently;
    grompp checks if tau_t is large enough
  * grompp by default sets the new nstpcouple parameter equal to
    nstlist, this means P-coupling is done less frequently;
    grompp checks if tau_p is large enough
  * mdrun results with old tpr files with twin-range non-bonded
    interactions will be different, because of the new symplectic
    integrator
  * for free-energy calculations sc-sigma now also sets the minimum
    soft-core sigma (old tpr files retain the old  behavior,
    which can be enforced by setting the env.var. GMX_SCSIGMA_MIN to 0)
This commit is contained in:
asau 2010-09-03 20:52:39 +00:00
parent 755c071d71
commit 1d63703b27
10 changed files with 548 additions and 267 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

7
biology/gromacs/Makefile
View file

@ -1,8 +1,7 @@
# $NetBSD: Makefile,v 1.3 2010/07/31 19:14:08 dholland Exp $
# $NetBSD: Makefile,v 1.4 2010/09/03 20:52:39 asau Exp $
#
DISTNAME= gromacs-4.0.7
PKGREVISION= 2
DISTNAME= gromacs-4.5.1
CATEGORIES= biology
MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/
@ -18,10 +17,12 @@ PKG_DESTDIR_SUPPORT= user-destdir
GNU_CONFIGURE= yes
USE_LIBTOOL= yes
USE_PKGLOCALEDIR= yes
USE_TOOLS+= pkg-config
CONFIGURE_ARGS+= --enable-shared
CONFIGURE_ARGS+= --enable-double --program-suffix=
CONFIGURE_ARGS+= --with-gsl
CONFIGURE_ARGS+= --disable-gcc41-check
.include "options.mk"

653
biology/gromacs/PLIST
View file

@ -1,9 +1,8 @@
@comment $NetBSD: PLIST,v 1.2 2010/05/16 12:04:03 asau Exp $
@comment $NetBSD: PLIST,v 1.3 2010/09/03 20:52:39 asau Exp $
bin/GMXRC
bin/GMXRC.bash
bin/GMXRC.csh
bin/GMXRC.zsh
bin/anadock
bin/completion.bash
bin/completion.csh
bin/completion.zsh
@ -11,9 +10,11 @@ bin/demux.pl
bin/do_dssp
bin/editconf
bin/eneconv
bin/g_anadock
bin/g_anaeig
bin/g_analyze
bin/g_angle
bin/g_bar
bin/g_bond
bin/g_bundle
bin/g_chi
@ -38,9 +39,10 @@ bin/g_h2order
bin/g_hbond
bin/g_helix
bin/g_helixorient
bin/g_kinetics
bin/g_lie
bin/g_luck
bin/g_mdmat
bin/g_membed
bin/g_mindist
bin/g_morph
bin/g_msd
@ -48,28 +50,36 @@ bin/g_nmeig
bin/g_nmens
bin/g_nmtraj
bin/g_order
bin/g_pme_error
bin/g_polystat
bin/g_potential
bin/g_principal
bin/g_protonate
bin/g_rama
bin/g_rdf
bin/g_rms
bin/g_rmsdist
bin/g_rmsf
bin/g_rotacf
bin/g_rotmat
bin/g_saltbr
bin/g_sas
bin/g_sdf
bin/g_select
bin/g_sgangle
bin/g_sham
bin/g_sigeps
bin/g_sorient
bin/g_spatial
bin/g_spol
bin/g_tcaf
bin/g_traj
bin/g_tune_pme
bin/g_vanhove
bin/g_velacc
bin/g_wham
bin/g_wheel
bin/g_x2top
${PLIST.x11}bin/g_xrama
bin/genbox
bin/genconf
bin/genion
@ -77,25 +87,18 @@ bin/genrestr
bin/gmxcheck
bin/gmxdump
bin/grompp
${PLIST.x11}bin/highway
bin/luck
bin/make_edi
bin/make_ndx
bin/mdrun
bin/mk_angndx
${PLIST.x11}bin/ngmx
bin/pdb2gmx
bin/protonate
bin/sigeps
bin/tpbconv
bin/trjcat
bin/trjconv
bin/trjorder
bin/wheel
bin/x2top
bin/xplor2gmx.pl
bin/xpm2ps
${PLIST.x11}bin/xrama
include/gromacs/3dview.h
include/gromacs/assert.h
include/gromacs/atomprop.h
@ -103,12 +106,15 @@ include/gromacs/bondf.h
include/gromacs/calcgrid.h
include/gromacs/calch.h
include/gromacs/calcmu.h
include/gromacs/centerofmass.h
include/gromacs/chargegroup.h
include/gromacs/checkpoint.h
include/gromacs/confio.h
include/gromacs/constr.h
include/gromacs/copyrite.h
include/gromacs/coulomb.h
include/gromacs/dihre.h
include/gromacs/displacement.h
include/gromacs/disre.h
include/gromacs/do_fit.h
include/gromacs/domdec.h
@ -117,45 +123,60 @@ include/gromacs/ebin.h
include/gromacs/edsam.h
include/gromacs/enxio.h
include/gromacs/ffscanf.h
include/gromacs/fftgrid.h
include/gromacs/filenm.h
include/gromacs/force.h
include/gromacs/futil.h
include/gromacs/gbutil.h
include/gromacs/gen_ad.h
include/gromacs/genborn.h
include/gromacs/gmx_ana.h
include/gromacs/gmx_arpack.h
include/gromacs/gmx_blas.h
include/gromacs/gmx_cyclecounter.h
include/gromacs/gmx_fatal.h
include/gromacs/gmx_fft.h
include/gromacs/gmx_ga2la.h
include/gromacs/gmx_lapack.h
include/gromacs/gmx_matrix.h
include/gromacs/gmx_parallel_3dfft.h
include/gromacs/gmx_random.h
include/gromacs/gmx_sort.h
include/gromacs/gmx_sse2_double.h
include/gromacs/gmx_sse2_single.h
include/gromacs/gmx_statistics.h
include/gromacs/gmx_system_xdr.h
include/gromacs/gmx_thread.h
include/gromacs/gmx_wallcycle.h
include/gromacs/gmxcomplex.h
include/gromacs/gmxcpp.h
include/gromacs/gmxfio.h
include/gromacs/gpp_atomtype.h
include/gromacs/gpp_nextnb.h
include/gromacs/grompp.h
include/gromacs/gstat.h
include/gromacs/hackblock.h
include/gromacs/histogram.h
include/gromacs/index.h
include/gromacs/indexutil.h
include/gromacs/inputrec.h
include/gromacs/invblock.h
include/gromacs/macros.h
include/gromacs/magic.h
include/gromacs/main.h
include/gromacs/mainpage.h
include/gromacs/maths.h
include/gromacs/matio.h
include/gromacs/md5.h
include/gromacs/mdatoms.h
include/gromacs/mdebin.h
include/gromacs/mdrun.h
include/gromacs/molfile_plugin.h
include/gromacs/mpelogging.h
include/gromacs/mshift.h
include/gromacs/mtop_util.h
include/gromacs/mtxio.h
include/gromacs/mvdata.h
include/gromacs/names.h
include/gromacs/nbsearch.h
include/gromacs/network.h
include/gromacs/nonbonded.h
include/gromacs/nrama.h
@ -163,14 +184,17 @@ include/gromacs/nrjac.h
include/gromacs/nrnb.h
include/gromacs/ns.h
include/gromacs/nsgrid.h
include/gromacs/oenv.h
include/gromacs/orires.h
include/gromacs/partdec.h
include/gromacs/pbc.h
include/gromacs/pdb2top.h
include/gromacs/pdbio.h
include/gromacs/pdebug.h
include/gromacs/perf_est.h
include/gromacs/physics.h
include/gromacs/pme.h
include/gromacs/poscalc.h
include/gromacs/position.h
include/gromacs/pppm.h
include/gromacs/princ.h
include/gromacs/pull.h
@ -178,29 +202,54 @@ include/gromacs/qmmm.h
include/gromacs/random.h
include/gromacs/rbin.h
include/gromacs/rdgroup.h
include/gromacs/readcomp.h
include/gromacs/readinp.h
include/gromacs/reorder.h
include/gromacs/resall.h
include/gromacs/rmpbc.h
include/gromacs/selection.h
include/gromacs/selmethod.h
include/gromacs/selparam.h
include/gromacs/selvalue.h
include/gromacs/sfactor.h
include/gromacs/shellfc.h
include/gromacs/shift.h
include/gromacs/sighandler.h
include/gromacs/smalloc.h
include/gromacs/sortwater.h
include/gromacs/sparsematrix.h
include/gromacs/split.h
include/gromacs/splitter.h
include/gromacs/statusio.h
include/gromacs/statutil.h
include/gromacs/strdb.h
include/gromacs/string2.h
include/gromacs/struc2.h
include/gromacs/symtab.h
include/gromacs/sysstuff.h
include/gromacs/tags.h
include/gromacs/tgroup.h
include/gromacs/thread_mpi.h
include/gromacs/thread_mpi/atomic.h
include/gromacs/thread_mpi/atomic/gcc.h
include/gromacs/thread_mpi/atomic/gcc_ia64.h
include/gromacs/thread_mpi/atomic/gcc_intrinsics.h
include/gromacs/thread_mpi/atomic/gcc_ppc.h
include/gromacs/thread_mpi/atomic/gcc_spinlock.h
include/gromacs/thread_mpi/atomic/gcc_x86.h
include/gromacs/thread_mpi/atomic/hpux.h
include/gromacs/thread_mpi/atomic/msvc.h
include/gromacs/thread_mpi/atomic/xlc_ppc.h
include/gromacs/thread_mpi/barrier.h
include/gromacs/thread_mpi/collective.h
include/gromacs/thread_mpi/event.h
include/gromacs/thread_mpi/hwinfo.h
include/gromacs/thread_mpi/list.h
include/gromacs/thread_mpi/lock.h
include/gromacs/thread_mpi/mpi_bindings.h
include/gromacs/thread_mpi/threads.h
include/gromacs/thread_mpi/tmpi.h
include/gromacs/thread_mpi/wait.h
include/gromacs/tmpi.h
include/gromacs/topsort.h
include/gromacs/toputil.h
include/gromacs/tpxio.h
include/gromacs/transfer.h
include/gromacs/trajana.h
include/gromacs/trnio.h
include/gromacs/txtdump.h
include/gromacs/typedefs.h
@ -213,6 +262,7 @@ include/gromacs/types/enums.h
include/gromacs/types/fcdata.h
include/gromacs/types/filenm.h
include/gromacs/types/forcerec.h
include/gromacs/types/genborn.h
include/gromacs/types/graph.h
include/gromacs/types/group.h
include/gromacs/types/idef.h
@ -222,10 +272,10 @@ include/gromacs/types/ishift.h
include/gromacs/types/matrix.h
include/gromacs/types/mdatom.h
include/gromacs/types/nblist.h
include/gromacs/types/nbslist.h
include/gromacs/types/nrnb.h
include/gromacs/types/ns.h
include/gromacs/types/nsgrid.h
include/gromacs/types/oenv.h
include/gromacs/types/pbc.h
include/gromacs/types/qmmmrec.h
include/gromacs/types/shellfc.h
@ -235,11 +285,14 @@ include/gromacs/types/symtab.h
include/gromacs/types/topology.h
include/gromacs/types/trx.h
include/gromacs/update.h
include/gromacs/utils.h
include/gromacs/vcm.h
include/gromacs/vec.h
include/gromacs/viewit.h
include/gromacs/vmddlopen.h
include/gromacs/vmdio.h
include/gromacs/vmdplugin.h
include/gromacs/vsite.h
include/gromacs/warninp.h
include/gromacs/wgms.h
include/gromacs/wman.h
include/gromacs/writeps.h
@ -248,14 +301,20 @@ include/gromacs/xtcio.h
include/gromacs/xvgr.h
lib/libgmx${MPI}_d.la
lib/libgmxana${MPI}_d.la
lib/libgmxpreprocess${MPI}_d.la
lib/libmd${MPI}_d.la
man/man1/anadock.1
lib/pkgconfig/libgmx${MPI}_d.pc
lib/pkgconfig/libgmxana${MPI}_d.pc
lib/pkgconfig/libgmxpreprocess${MPI}_d.pc
lib/pkgconfig/libmd${MPI}_d.pc
man/man1/do_dssp.1
man/man1/editconf.1
man/man1/eneconv.1
man/man1/g_anadock.1
man/man1/g_anaeig.1
man/man1/g_analyze.1
man/man1/g_angle.1
man/man1/g_bar.1
man/man1/g_bond.1
man/man1/g_bundle.1
man/man1/g_chi.1
@ -280,9 +339,9 @@ man/man1/g_h2order.1
man/man1/g_hbond.1
man/man1/g_helix.1
man/man1/g_helixorient.1
man/man1/g_kinetics.1
man/man1/g_lie.1
man/man1/g_mdmat.1
man/man1/g_membed.1
man/man1/g_mindist.1
man/man1/g_morph.1
man/man1/g_msd.1
@ -293,26 +352,32 @@ man/man1/g_order.1
man/man1/g_polystat.1
man/man1/g_potential.1
man/man1/g_principal.1
man/man1/g_protonate.1
man/man1/g_rama.1
man/man1/g_rdf.1
man/man1/g_rms.1
man/man1/g_rmsdist.1
man/man1/g_rmsf.1
man/man1/g_rotacf.1
man/man1/g_rotmat.1
man/man1/g_saltbr.1
man/man1/g_sas.1
man/man1/g_sdf.1
man/man1/g_select.1
man/man1/g_sgangle.1
man/man1/g_sham.1
man/man1/g_sigeps.1
man/man1/g_sorient.1
man/man1/g_spatial.1
man/man1/g_spol.1
man/man1/g_tcaf.1
man/man1/g_traj.1
man/man1/g_tune_pme.1
man/man1/g_vanhove.1
man/man1/g_velacc.1
man/man1/g_wham.1
man/man1/gen_table.1
man/man1/g_wheel.1
man/man1/g_x2top.1
man/man1/g_xrama.1
man/man1/genbox.1
man/man1/genconf.1
man/man1/genion.1
@ -320,23 +385,18 @@ man/man1/genrestr.1
man/man1/gmxcheck.1
man/man1/gmxdump.1
man/man1/grompp.1
man/man1/highway.1
man/man1/make_edi.1
man/man1/make_ndx.1
man/man1/mdrun.1
man/man1/mk_angndx.1
man/man1/ngmx.1
man/man1/pdb2gmx.1
man/man1/protonate.1
man/man1/sigeps.1
man/man1/tpbconv.1
man/man1/trjcat.1
man/man1/trjconv.1
man/man1/trjorder.1
man/man1/wheel.1
man/man1/x2top.1
man/man1/xpm2ps.1
man/man1/xrama.1
man/man7/gromacs.7
share/gromacs/html/gmxfaq.html
share/gromacs/html/images/1ctf-0.2.jpg
share/gromacs/html/images/1ctf-0.5.jpg
@ -493,142 +553,467 @@ share/gromacs/html/online/xtc.html
share/gromacs/html/online/xvg.html
share/gromacs/html/online/yourown.html
share/gromacs/template/Makefile.${MACHINE_GNU_PLATFORM}_double
share/gromacs/template/Makefile.pkg
share/gromacs/template/README
share/gromacs/template/template.c
share/gromacs/top/1mlg.itp
share/gromacs/top/2mlg.itp
share/gromacs/top/FF.dat
share/gromacs/top/aminoacids.dat
share/gromacs/top/amber03.ff/aminoacids.arn
share/gromacs/top/amber03.ff/aminoacids.c.tdb
share/gromacs/top/amber03.ff/aminoacids.hdb
share/gromacs/top/amber03.ff/aminoacids.n.tdb
share/gromacs/top/amber03.ff/aminoacids.r2b
share/gromacs/top/amber03.ff/aminoacids.rtp
share/gromacs/top/amber03.ff/aminoacids.vsd
share/gromacs/top/amber03.ff/atomtypes.atp
share/gromacs/top/amber03.ff/dna.arn
share/gromacs/top/amber03.ff/dna.hdb
share/gromacs/top/amber03.ff/dna.r2b
share/gromacs/top/amber03.ff/dna.rtp
share/gromacs/top/amber03.ff/ffbonded.itp
share/gromacs/top/amber03.ff/ffnonbonded.itp
share/gromacs/top/amber03.ff/forcefield.doc
share/gromacs/top/amber03.ff/forcefield.itp
share/gromacs/top/amber03.ff/gbsa.itp
share/gromacs/top/amber03.ff/ions.itp
share/gromacs/top/amber03.ff/rna.arn
share/gromacs/top/amber03.ff/rna.hdb
share/gromacs/top/amber03.ff/rna.r2b
share/gromacs/top/amber03.ff/rna.rtp
share/gromacs/top/amber03.ff/spc.itp
share/gromacs/top/amber03.ff/spce.itp
share/gromacs/top/amber03.ff/tip3p.itp
share/gromacs/top/amber03.ff/tip4p.itp
share/gromacs/top/amber03.ff/tip4pew.itp
share/gromacs/top/amber03.ff/tip5p.itp
share/gromacs/top/amber03.ff/urea.itp
share/gromacs/top/amber03.ff/watermodels.dat
share/gromacs/top/amber94.ff/aminoacids.arn
share/gromacs/top/amber94.ff/aminoacids.c.tdb
share/gromacs/top/amber94.ff/aminoacids.hdb
share/gromacs/top/amber94.ff/aminoacids.n.tdb
share/gromacs/top/amber94.ff/aminoacids.r2b
share/gromacs/top/amber94.ff/aminoacids.rtp
share/gromacs/top/amber94.ff/aminoacids.vsd
share/gromacs/top/amber94.ff/atomtypes.atp
share/gromacs/top/amber94.ff/dna.arn
share/gromacs/top/amber94.ff/dna.hdb
share/gromacs/top/amber94.ff/dna.r2b
share/gromacs/top/amber94.ff/dna.rtp
share/gromacs/top/amber94.ff/ffbonded.itp
share/gromacs/top/amber94.ff/ffnonbonded.itp
share/gromacs/top/amber94.ff/forcefield.doc
share/gromacs/top/amber94.ff/forcefield.itp
share/gromacs/top/amber94.ff/gbsa.itp
share/gromacs/top/amber94.ff/ions.itp
share/gromacs/top/amber94.ff/rna.arn
share/gromacs/top/amber94.ff/rna.hdb
share/gromacs/top/amber94.ff/rna.r2b
share/gromacs/top/amber94.ff/rna.rtp
share/gromacs/top/amber94.ff/spc.itp
share/gromacs/top/amber94.ff/spce.itp
share/gromacs/top/amber94.ff/tip3p.itp
share/gromacs/top/amber94.ff/tip4p.itp
share/gromacs/top/amber94.ff/tip4pew.itp
share/gromacs/top/amber94.ff/tip5p.itp
share/gromacs/top/amber94.ff/urea.itp
share/gromacs/top/amber94.ff/watermodels.dat
share/gromacs/top/amber96.ff/aminoacids.arn
share/gromacs/top/amber96.ff/aminoacids.c.tdb
share/gromacs/top/amber96.ff/aminoacids.hdb
share/gromacs/top/amber96.ff/aminoacids.n.tdb
share/gromacs/top/amber96.ff/aminoacids.r2b
share/gromacs/top/amber96.ff/aminoacids.rtp
share/gromacs/top/amber96.ff/aminoacids.vsd
share/gromacs/top/amber96.ff/atomtypes.atp
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share/gromacs/top/gromos43a2.ff/watermodels.dat
share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb
share/gromacs/top/gromos45a3.ff/aminoacids.hdb
share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb
share/gromacs/top/gromos45a3.ff/aminoacids.r2b
share/gromacs/top/gromos45a3.ff/aminoacids.rtp
share/gromacs/top/gromos45a3.ff/aminoacids.vsd
share/gromacs/top/gromos45a3.ff/atomtypes.atp
share/gromacs/top/gromos45a3.ff/ff_dum.itp
share/gromacs/top/gromos45a3.ff/ffbonded.itp
share/gromacs/top/gromos45a3.ff/ffnonbonded.itp
share/gromacs/top/gromos45a3.ff/forcefield.doc
share/gromacs/top/gromos45a3.ff/forcefield.itp
share/gromacs/top/gromos45a3.ff/ions.itp
share/gromacs/top/gromos45a3.ff/spc.itp
share/gromacs/top/gromos45a3.ff/spce.itp
share/gromacs/top/gromos45a3.ff/tip3p.itp
share/gromacs/top/gromos45a3.ff/tip4p.itp
share/gromacs/top/gromos45a3.ff/watermodels.dat
share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb
share/gromacs/top/gromos53a5.ff/aminoacids.hdb
share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb
share/gromacs/top/gromos53a5.ff/aminoacids.r2b
share/gromacs/top/gromos53a5.ff/aminoacids.rtp
share/gromacs/top/gromos53a5.ff/aminoacids.vsd
share/gromacs/top/gromos53a5.ff/atomname2type.n2t
share/gromacs/top/gromos53a5.ff/atomtypes.atp
share/gromacs/top/gromos53a5.ff/ff_dum.itp
share/gromacs/top/gromos53a5.ff/ffbonded.itp
share/gromacs/top/gromos53a5.ff/ffnonbonded.itp
share/gromacs/top/gromos53a5.ff/forcefield.doc
share/gromacs/top/gromos53a5.ff/forcefield.itp
share/gromacs/top/gromos53a5.ff/ions.itp
share/gromacs/top/gromos53a5.ff/spc.itp
share/gromacs/top/gromos53a5.ff/spce.itp
share/gromacs/top/gromos53a5.ff/tip3p.itp
share/gromacs/top/gromos53a5.ff/tip4p.itp
share/gromacs/top/gromos53a5.ff/watermodels.dat
share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
share/gromacs/top/gromos53a6.ff/aminoacids.hdb
share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
share/gromacs/top/gromos53a6.ff/aminoacids.r2b
share/gromacs/top/gromos53a6.ff/aminoacids.rtp
share/gromacs/top/gromos53a6.ff/aminoacids.vsd
share/gromacs/top/gromos53a6.ff/atomtypes.atp
share/gromacs/top/gromos53a6.ff/ff_dum.itp
share/gromacs/top/gromos53a6.ff/ffbonded.itp
share/gromacs/top/gromos53a6.ff/ffnonbonded.itp
share/gromacs/top/gromos53a6.ff/forcefield.doc
share/gromacs/top/gromos53a6.ff/forcefield.itp
share/gromacs/top/gromos53a6.ff/ions.itp
share/gromacs/top/gromos53a6.ff/spc.itp
share/gromacs/top/gromos53a6.ff/spce.itp
share/gromacs/top/gromos53a6.ff/tip3p.itp
share/gromacs/top/gromos53a6.ff/tip4p.itp
share/gromacs/top/gromos53a6.ff/watermodels.dat
share/gromacs/top/gurgle.dat
share/gromacs/top/h2p4o13.itp
share/gromacs/top/h2p8o25.itp
share/gromacs/top/h2po4.itp
share/gromacs/top/ha-shift.dat
share/gromacs/top/highway.dat
share/gromacs/top/ions.itp
share/gromacs/top/links.dat
share/gromacs/top/methanol.itp
share/gromacs/top/oplsaa.ff/1propanol.itp
share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
share/gromacs/top/oplsaa.ff/aminoacids.hdb
share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
share/gromacs/top/oplsaa.ff/aminoacids.r2b
share/gromacs/top/oplsaa.ff/aminoacids.rtp
share/gromacs/top/oplsaa.ff/aminoacids.vsd
share/gromacs/top/oplsaa.ff/atomname2type.n2t
share/gromacs/top/oplsaa.ff/atomtypes.atp
share/gromacs/top/oplsaa.ff/ethanol.itp
share/gromacs/top/oplsaa.ff/ffbonded.itp
share/gromacs/top/oplsaa.ff/ffnonbonded.itp
share/gromacs/top/oplsaa.ff/forcefield.doc
share/gromacs/top/oplsaa.ff/forcefield.itp
share/gromacs/top/oplsaa.ff/gbsa.itp
share/gromacs/top/oplsaa.ff/ions.itp
share/gromacs/top/oplsaa.ff/methanol.itp
share/gromacs/top/oplsaa.ff/spc.itp
share/gromacs/top/oplsaa.ff/spce.itp
share/gromacs/top/oplsaa.ff/tip3p.itp
share/gromacs/top/oplsaa.ff/tip4p.itp
share/gromacs/top/oplsaa.ff/tip5p.itp
share/gromacs/top/oplsaa.ff/watermodels.dat
share/gromacs/top/phbres.dat
share/gromacs/top/ps.m2p
share/gromacs/top/random.dat
share/gromacs/top/refi_aa.dat
share/gromacs/top/residuetypes.dat
share/gromacs/top/sfactor.dat
share/gromacs/top/spc.itp
share/gromacs/top/spc216.gro
share/gromacs/top/spce.itp
@ -641,14 +1026,10 @@ share/gromacs/top/table6-11.xvg
share/gromacs/top/table6-12.xvg
share/gromacs/top/table6-8.xvg
share/gromacs/top/table6-9.xvg
share/gromacs/top/tfe.itp
share/gromacs/top/tip3p.itp
share/gromacs/top/tip4p.gro
share/gromacs/top/tip4p.itp
share/gromacs/top/tip5p.gro
share/gromacs/top/tip5p.itp
share/gromacs/top/urea+h2o.gro
share/gromacs/top/urea.itp
share/gromacs/top/vdwradii.dat
share/gromacs/top/xlateat.dat
share/gromacs/tutor/gmxdemo/cpeptide.pdb

18
biology/gromacs/distinfo
View file

@ -1,16 +1,12 @@
$NetBSD: distinfo,v 1.4 2010/07/31 19:14:08 dholland Exp $
$NetBSD: distinfo,v 1.5 2010/09/03 20:52:39 asau Exp $
SHA1 (gromacs-4.0.7.tar.gz) = 8519bef2fa989fb487d54612b0a2d0228f228b30
RMD160 (gromacs-4.0.7.tar.gz) = 4fa8e5c90f549ef627a98a907a166676692a4c4b
Size (gromacs-4.0.7.tar.gz) = 8404518 bytes
SHA1 (patch-aa) = dcf39e862c2087bca0cd4e577438633bf70fe57f
SHA1 (patch-ab) = 333fea1f0844f8628795f593de16c941744b11d2
SHA1 (patch-ac) = 164a7b3e06ab4f4cc1142615c1281eec82adee9b
SHA1 (gromacs-4.5.1.tar.gz) = 4352565278e39fb619208950780d8cb0b470a200
RMD160 (gromacs-4.5.1.tar.gz) = b28973526859359c84ba5d4fe2a5018b158f932b
Size (gromacs-4.5.1.tar.gz) = 10300446 bytes
SHA1 (patch-aa) = 29c6683c71989621f0f41682b1c225f524a2d84f
SHA1 (patch-ad) = 68b37154ba466e28cad0e539e25253c901421aaa
SHA1 (patch-ae) = 59a5e88abeee883483b557cab1681c9a9098870f
SHA1 (patch-af) = 58e97df84e64e071257fd36d09840ef719461ea5
SHA1 (patch-ag) = 5d46a0dba7db4dbf08ea83d448a6e5201871d217
SHA1 (patch-ah) = ad930cbb9f448780ca8745b899fe54c5470fff3b
SHA1 (patch-ag) = 810d58d3ad787c9508f775674541775245402596
SHA1 (patch-ah) = 36ceeb409e59d8d3f0abe3bfa3ea3108f61f7a8e
SHA1 (patch-ai) = ed4aa71eb56d1300c67cd17057f72ea452739f3d
SHA1 (patch-aj) = 080d2923d729ff00de0f2cae75a82ec6c3769d6c
SHA1 (patch-ak) = bdfebf85422a6a9025d1f2c71921c4cc1c3069c4

20
biology/gromacs/patches/patch-aa
View file

@ -1,19 +1,19 @@
$NetBSD: patch-aa,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $
$NetBSD: patch-aa,v 1.2 2010/09/03 20:52:39 asau Exp $
Allow flags to contain commas.
--- share/template/Makefile.in.orig 2010-01-12 15:44:18.000000000 +0300
+++ share/template/Makefile.in 2010-01-12 15:58:57.000000000 +0300
@@ -389,9 +389,9 @@
--- share/template/Makefile.in.orig 2010-08-10 22:56:17.000000000 +0400
+++ share/template/Makefile.in 2010-08-11 00:14:07.000000000 +0400
@@ -569,9 +569,9 @@
Makefile.@host@ Makefile.@host@_double: Template.mak Makefile
cat $(srcdir)/Template.mak | \
- sed 's,@LDFLAGS\@,$(LDFLAGS),' | \
- sed 's,@LIBS\@,$(LIBS),' | \
- sed 's,@LDFLAGS\@,$(XLDFLAGS),' | \
- sed 's,@LIBS\@,$(XLIBS),' | \
- sed 's,@CFLAGS\@,$(MYCFLAGS),' | \
+ sed 's|@LDFLAGS\@|$(LDFLAGS)|' | \
+ sed 's|@LIBS\@|$(LIBS)|' | \
+ sed 's|@LDFLAGS\@|$(XLDFLAGS)|' | \
+ sed 's|@LIBS\@|$(XLIBS)|' | \
+ sed 's|@CFLAGS\@|$(MYCFLAGS)|' | \
sed 's,@CC\@,$(CC),' | \
sed 's,@CC\@,$(XCC),' | \
sed 's,@host\@,@host@,' >$@
# Tell versions [3.59,3.63) of GNU make to not export all variables.
#template.$(OBJEXT): gromacs

24
biology/gromacs/patches/patch-ab
View file

@ -1,24 +0,0 @@
$NetBSD: patch-ab,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $
Avoid non-standard "==" in test.
--- configure.ac.orig 2009-12-07 00:18:27.000000000 +0300
+++ configure.ac 2010-03-15 16:02:27.000000000 +0300
@@ -183,7 +183,7 @@
[set --enable-ppc-sqrt=1 for better speed.])],,
enable_ppc_sqrt=no)
if test "$enable_ppc_sqrt" != "no"; then
- if test "$enable_ppc_sqrt" == "1"; then
+ if test "$enable_ppc_sqrt" = "1"; then
ppc_sqrt_niter=1;
else
ppc_sqrt_niter=2;
@@ -193,7 +193,7 @@
enable_software_sqrt="no";
fi
AM_CONDITIONAL([GMX_POWERPC_SQRT],[test "$enable_ppc_sqrt" != "no"])
-AM_CONDITIONAL([GMX_POWERPC_SQRT_SINGLE_ITERATION],[test "$ppc_sqrt_niter" == "1"])
+AM_CONDITIONAL([GMX_POWERPC_SQRT_SINGLE_ITERATION],[test "$ppc_sqrt_niter" = "1"])
if test "$enable_software_sqrt" = "yes"; then

24
biology/gromacs/patches/patch-ac
View file

@ -1,24 +0,0 @@
$NetBSD: patch-ac,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $
Avoid non-standard "==" in test.
--- configure.orig 2010-03-15 15:59:18.000000000 +0300
+++ configure 2010-03-15 16:00:44.000000000 +0300
@@ -2994,7 +2994,7 @@
fi
if test "$enable_ppc_sqrt" != "no"; then
- if test "$enable_ppc_sqrt" == "1"; then
+ if test "$enable_ppc_sqrt" = "1"; then
ppc_sqrt_niter=1;
else
ppc_sqrt_niter=2;
@@ -3015,7 +3015,7 @@
GMX_POWERPC_SQRT_FALSE=
fi
- if test "$ppc_sqrt_niter" == "1"; then
+ if test "$ppc_sqrt_niter" = "1"; then
GMX_POWERPC_SQRT_SINGLE_ITERATION_TRUE=
GMX_POWERPC_SQRT_SINGLE_ITERATION_FALSE='#'
else

15
biology/gromacs/patches/patch-af
View file

@ -1,15 +0,0 @@
$NetBSD: patch-af,v 1.1 2010/06/17 09:26:16 asau Exp $
Modern libtool requires tag.
--- src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile.in.orig 2009-12-06 21:18:53.000000000 +0000
+++ src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile.in 2010-06-17 07:53:47.000000000 +0000
@@ -69,7 +69,7 @@
--mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \
$(LDFLAGS) -o $@
CCASCOMPILE = $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS)
-LTCCASCOMPILE = $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+LTCCASCOMPILE = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=compile $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS)
SOURCES = $(libnb_kernel_ia32_3dnow_la_SOURCES)
DIST_SOURCES = $(libnb_kernel_ia32_3dnow_la_SOURCES)

10
biology/gromacs/patches/patch-ag
View file

@ -1,11 +1,11 @@
$NetBSD: patch-ag,v 1.1 2010/06/17 09:26:16 asau Exp $
$NetBSD: patch-ag,v 1.2 2010/09/03 20:52:39 asau Exp $
Modern libtool requires tag.
--- src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile.in.orig 2009-12-06 21:18:53.000000000 +0000
+++ src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile.in 2010-06-17 07:56:36.000000000 +0000
@@ -67,7 +67,7 @@
am__depfiles_maybe = depfiles
--- src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile.in.orig 2010-07-30 22:55:04.000000000 +0400
+++ src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile.in 2010-07-31 11:57:35.000000000 +0400
@@ -71,7 +71,7 @@
am__mv = mv -f
CPPASCOMPILE = $(CCAS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CCASFLAGS) $(CCASFLAGS)
-LTCPPASCOMPILE = $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \

10
biology/gromacs/patches/patch-ah
View file

@ -1,11 +1,11 @@
$NetBSD: patch-ah,v 1.1 2010/06/17 09:26:16 asau Exp $
$NetBSD: patch-ah,v 1.2 2010/09/03 20:52:39 asau Exp $
Modern libtool requires tag.
--- src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile.in.orig 2009-12-06 21:18:54.000000000 +0000
+++ src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile.in 2010-06-17 07:57:43.000000000 +0000
@@ -67,7 +67,7 @@
am__depfiles_maybe = depfiles
--- src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile.in.orig 2010-07-30 22:55:04.000000000 +0400
+++ src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile.in 2010-07-31 11:58:30.000000000 +0400
@@ -71,7 +71,7 @@
am__mv = mv -f
CPPASCOMPILE = $(CCAS) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
$(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CCASFLAGS) $(CCASFLAGS)
-LTCPPASCOMPILE = $(LIBTOOL) $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \

34
biology/gromacs/patches/patch-ak
View file

@ -1,34 +0,0 @@
$NetBSD: patch-ak,v 1.1 2010/07/31 19:14:08 dholland Exp $
Disable the extra symlinks like in src/gmxlib/Makefile.in; this makes
the install behavior uniform for all the libraries.
Note that if re-enabled the references to "libdir" below need DESTDIR
affixed, or it'll blow up if USE_DESTDIR is set.
--- src/tools/Makefile.in.orig 2009-12-06 21:18:54.000000000 +0000
+++ src/tools/Makefile.in
@@ -1407,14 +1407,14 @@ uninstall-am: uninstall-binPROGRAMS unin
# link the mpi library to non-mpi names if the latter are not present
-install-exec-hook:
- libname="libgmxana@LIBSUFFIX@"; \
- nompi="`echo $$libname | sed -e 's,_mpi,,'`"; \
- libdir="$(libdir)"; \
- if echo $$libname | grep mpi >/dev/null ; then \
- (cd $$libdir && test -e $$libname.a -a ! -e $$nompi.a && $(LN_S) $$libname.a $$nompi.a ; exit 0); \
- (cd $$libdir && test -e $$libname.so -a ! -e $$nompi.so && $(LN_S) $$libname.so $$nompi.so ; exit 0); \
- fi;
+install-exec-hook: ;
+# libname="libgmxana@LIBSUFFIX@"; \
+# nompi="`echo $$libname | sed -e 's,_mpi,,'`"; \
+# libdir="$(libdir)"; \
+# if echo $$libname | grep mpi >/dev/null ; then \
+# (cd $$libdir && test -e $$libname.a -a ! -e $$nompi.a && $(LN_S) $$libname.a $$nompi.a ; exit 0); \
+# (cd $$libdir && test -e $$libname.so -a ! -e $$nompi.so && $(LN_S) $$libname.so $$nompi.so ; exit 0); \
+# fi;
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT: