Update to GROMACS 4.5.1

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)

10 files changed, 548 insertions, 267 deletions

diff --git a/biology/gromacs/Makefile b/biology/gromacs/Makefile
index c9646e837c2..3e9e8da5d55 100644
--- a/biology/gromacs/Makefile
+++ b/biology/gromacs/Makefile
@@ -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"
 
diff --git a/biology/gromacs/PLIST b/biology/gromacs/PLIST
index 4fc7f1146ba..fd58b375648 100644
--- a/biology/gromacs/PLIST
+++ b/biology/gromacs/PLIST
@@ -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
+share/gromacs/top/amber96.ff/dna.arn
+share/gromacs/top/amber96.ff/dna.hdb
+share/gromacs/top/amber96.ff/dna.r2b
+share/gromacs/top/amber96.ff/dna.rtp
+share/gromacs/top/amber96.ff/ffbonded.itp
+share/gromacs/top/amber96.ff/ffnonbonded.itp
+share/gromacs/top/amber96.ff/forcefield.doc
+share/gromacs/top/amber96.ff/forcefield.itp
+share/gromacs/top/amber96.ff/gbsa.itp
+share/gromacs/top/amber96.ff/ions.itp
+share/gromacs/top/amber96.ff/rna.arn
+share/gromacs/top/amber96.ff/rna.hdb
+share/gromacs/top/amber96.ff/rna.r2b
+share/gromacs/top/amber96.ff/rna.rtp
+share/gromacs/top/amber96.ff/spc.itp
+share/gromacs/top/amber96.ff/spce.itp
+share/gromacs/top/amber96.ff/tip3p.itp
+share/gromacs/top/amber96.ff/tip4p.itp
+share/gromacs/top/amber96.ff/tip4pew.itp
+share/gromacs/top/amber96.ff/tip5p.itp
+share/gromacs/top/amber96.ff/urea.itp
+share/gromacs/top/amber96.ff/watermodels.dat
+share/gromacs/top/amber99.ff/aminoacids.arn
+share/gromacs/top/amber99.ff/aminoacids.c.tdb
+share/gromacs/top/amber99.ff/aminoacids.hdb
+share/gromacs/top/amber99.ff/aminoacids.n.tdb
+share/gromacs/top/amber99.ff/aminoacids.r2b
+share/gromacs/top/amber99.ff/aminoacids.rtp
+share/gromacs/top/amber99.ff/aminoacids.vsd
+share/gromacs/top/amber99.ff/atomtypes.atp
+share/gromacs/top/amber99.ff/dna.arn
+share/gromacs/top/amber99.ff/dna.hdb
+share/gromacs/top/amber99.ff/dna.r2b
+share/gromacs/top/amber99.ff/dna.rtp
+share/gromacs/top/amber99.ff/ffbonded.itp
+share/gromacs/top/amber99.ff/ffnonbonded.itp
+share/gromacs/top/amber99.ff/forcefield.doc
+share/gromacs/top/amber99.ff/forcefield.itp
+share/gromacs/top/amber99.ff/gbsa.itp
+share/gromacs/top/amber99.ff/ions.itp
+share/gromacs/top/amber99.ff/rna.arn
+share/gromacs/top/amber99.ff/rna.hdb
+share/gromacs/top/amber99.ff/rna.r2b
+share/gromacs/top/amber99.ff/rna.rtp
+share/gromacs/top/amber99.ff/spc.itp
+share/gromacs/top/amber99.ff/spce.itp
+share/gromacs/top/amber99.ff/tip3p.itp
+share/gromacs/top/amber99.ff/tip4p.itp
+share/gromacs/top/amber99.ff/tip4pew.itp
+share/gromacs/top/amber99.ff/tip5p.itp
+share/gromacs/top/amber99.ff/urea.itp
+share/gromacs/top/amber99.ff/watermodels.dat
+share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
+share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb
+share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
+share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
+share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b
+share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
+share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd
+share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
+share/gromacs/top/amber99sb-ildn.ff/dna.arn
+share/gromacs/top/amber99sb-ildn.ff/dna.hdb
+share/gromacs/top/amber99sb-ildn.ff/dna.r2b
+share/gromacs/top/amber99sb-ildn.ff/dna.rtp
+share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp
+share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp
+share/gromacs/top/amber99sb-ildn.ff/forcefield.doc
+share/gromacs/top/amber99sb-ildn.ff/forcefield.itp
+share/gromacs/top/amber99sb-ildn.ff/gbsa.itp
+share/gromacs/top/amber99sb-ildn.ff/ions.itp
+share/gromacs/top/amber99sb-ildn.ff/rna.arn
+share/gromacs/top/amber99sb-ildn.ff/rna.hdb
+share/gromacs/top/amber99sb-ildn.ff/rna.r2b
+share/gromacs/top/amber99sb-ildn.ff/rna.rtp
+share/gromacs/top/amber99sb-ildn.ff/spc.itp
+share/gromacs/top/amber99sb-ildn.ff/spce.itp
+share/gromacs/top/amber99sb-ildn.ff/tip3p.itp
+share/gromacs/top/amber99sb-ildn.ff/tip4p.itp
+share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp
+share/gromacs/top/amber99sb-ildn.ff/tip5p.itp
+share/gromacs/top/amber99sb-ildn.ff/urea.itp
+share/gromacs/top/amber99sb-ildn.ff/watermodels.dat
+share/gromacs/top/amber99sb.ff/aminoacids.arn
+share/gromacs/top/amber99sb.ff/aminoacids.c.tdb
+share/gromacs/top/amber99sb.ff/aminoacids.hdb
+share/gromacs/top/amber99sb.ff/aminoacids.n.tdb
+share/gromacs/top/amber99sb.ff/aminoacids.r2b
+share/gromacs/top/amber99sb.ff/aminoacids.rtp
+share/gromacs/top/amber99sb.ff/aminoacids.vsd
+share/gromacs/top/amber99sb.ff/atomtypes.atp
+share/gromacs/top/amber99sb.ff/dna.arn
+share/gromacs/top/amber99sb.ff/dna.hdb
+share/gromacs/top/amber99sb.ff/dna.r2b
+share/gromacs/top/amber99sb.ff/dna.rtp
+share/gromacs/top/amber99sb.ff/ffbonded.itp
+share/gromacs/top/amber99sb.ff/ffnonbonded.itp
+share/gromacs/top/amber99sb.ff/forcefield.doc
+share/gromacs/top/amber99sb.ff/forcefield.itp
+share/gromacs/top/amber99sb.ff/gbsa.itp
+share/gromacs/top/amber99sb.ff/ions.itp
+share/gromacs/top/amber99sb.ff/rna.arn
+share/gromacs/top/amber99sb.ff/rna.hdb
+share/gromacs/top/amber99sb.ff/rna.r2b
+share/gromacs/top/amber99sb.ff/rna.rtp
+share/gromacs/top/amber99sb.ff/spc.itp
+share/gromacs/top/amber99sb.ff/spce.itp
+share/gromacs/top/amber99sb.ff/tip3p.itp
+share/gromacs/top/amber99sb.ff/tip4p.itp
+share/gromacs/top/amber99sb.ff/tip4pew.itp
+share/gromacs/top/amber99sb.ff/tip5p.itp
+share/gromacs/top/amber99sb.ff/urea.itp
+share/gromacs/top/amber99sb.ff/watermodels.dat
+share/gromacs/top/amberGS.ff/aminoacids.arn
+share/gromacs/top/amberGS.ff/aminoacids.c.tdb
+share/gromacs/top/amberGS.ff/aminoacids.hdb
+share/gromacs/top/amberGS.ff/aminoacids.n.tdb
+share/gromacs/top/amberGS.ff/aminoacids.r2b
+share/gromacs/top/amberGS.ff/aminoacids.rtp
+share/gromacs/top/amberGS.ff/aminoacids.vsd
+share/gromacs/top/amberGS.ff/atomtypes.atp
+share/gromacs/top/amberGS.ff/dna.arn
+share/gromacs/top/amberGS.ff/dna.hdb
+share/gromacs/top/amberGS.ff/dna.r2b
+share/gromacs/top/amberGS.ff/dna.rtp
+share/gromacs/top/amberGS.ff/ffbonded.itp
+share/gromacs/top/amberGS.ff/ffnonbonded.itp
+share/gromacs/top/amberGS.ff/forcefield.doc
+share/gromacs/top/amberGS.ff/forcefield.itp
+share/gromacs/top/amberGS.ff/gbsa.itp
+share/gromacs/top/amberGS.ff/ions.itp
+share/gromacs/top/amberGS.ff/rna.arn
+share/gromacs/top/amberGS.ff/rna.hdb
+share/gromacs/top/amberGS.ff/rna.r2b
+share/gromacs/top/amberGS.ff/rna.rtp
+share/gromacs/top/amberGS.ff/spc.itp
+share/gromacs/top/amberGS.ff/spce.itp
+share/gromacs/top/amberGS.ff/tip3p.itp
+share/gromacs/top/amberGS.ff/tip4p.itp
+share/gromacs/top/amberGS.ff/tip4pew.itp
+share/gromacs/top/amberGS.ff/tip5p.itp
+share/gromacs/top/amberGS.ff/urea.itp
+share/gromacs/top/amberGS.ff/watermodels.dat
 share/gromacs/top/atom_nom.tbl
 share/gromacs/top/atommass.dat
-share/gromacs/top/benzamide.itp
-share/gromacs/top/bondadd.itp
 share/gromacs/top/bonds.dlg
 share/gromacs/top/bromacs.dat
-share/gromacs/top/buck.itp
 share/gromacs/top/ca-shift.dat
 share/gromacs/top/cb-shift.dat
+share/gromacs/top/charmm27.ff/aminoacids.arn
+share/gromacs/top/charmm27.ff/aminoacids.c.tdb
+share/gromacs/top/charmm27.ff/aminoacids.hdb
+share/gromacs/top/charmm27.ff/aminoacids.n.tdb
+share/gromacs/top/charmm27.ff/aminoacids.r2b
+share/gromacs/top/charmm27.ff/aminoacids.rtp
+share/gromacs/top/charmm27.ff/aminoacids.vsd
+share/gromacs/top/charmm27.ff/atomtypes.atp
+share/gromacs/top/charmm27.ff/cmap.itp
+share/gromacs/top/charmm27.ff/dna.rtp
+share/gromacs/top/charmm27.ff/ffbonded.itp
+share/gromacs/top/charmm27.ff/ffnabonded.itp
+share/gromacs/top/charmm27.ff/ffnanonbonded.itp
+share/gromacs/top/charmm27.ff/ffnonbonded.itp
+share/gromacs/top/charmm27.ff/forcefield.doc
+share/gromacs/top/charmm27.ff/forcefield.itp
+share/gromacs/top/charmm27.ff/gb.itp
+share/gromacs/top/charmm27.ff/ions.itp
+share/gromacs/top/charmm27.ff/lipids.hdb
+share/gromacs/top/charmm27.ff/lipids.rtp
+share/gromacs/top/charmm27.ff/rna.rtp
+share/gromacs/top/charmm27.ff/spc.itp
+share/gromacs/top/charmm27.ff/spce.itp
+share/gromacs/top/charmm27.ff/tip3p.itp
+share/gromacs/top/charmm27.ff/tip4p.itp
+share/gromacs/top/charmm27.ff/tips3p.itp
+share/gromacs/top/charmm27.ff/watermodels.dat
 share/gromacs/top/co-shift.dat
-share/gromacs/top/dec50.gro
-share/gromacs/top/decane.itp
+share/gromacs/top/defselection.dat
 share/gromacs/top/dgsolv.dat
-share/gromacs/top/dlg.itp
-share/gromacs/top/dmso.gro
-share/gromacs/top/dmso.itp
 share/gromacs/top/edissoc.dat
 share/gromacs/top/electroneg.dat
 share/gromacs/top/elements.dat
+share/gromacs/top/encads.ff/aminoacids.c.tdb
+share/gromacs/top/encads.ff/aminoacids.hdb
+share/gromacs/top/encads.ff/aminoacids.n.tdb
+share/gromacs/top/encads.ff/aminoacids.r2b
+share/gromacs/top/encads.ff/aminoacids.rtp
+share/gromacs/top/encads.ff/atomtypes.atp
+share/gromacs/top/encads.ff/f3c.itp
+share/gromacs/top/encads.ff/ffbonded.itp
+share/gromacs/top/encads.ff/ffnonbonded.itp
+share/gromacs/top/encads.ff/forcefield.doc
+share/gromacs/top/encads.ff/forcefield.itp
+share/gromacs/top/encads.ff/watermodels.dat
+share/gromacs/top/encadv.ff/aminoacids.c.tdb
+share/gromacs/top/encadv.ff/aminoacids.hdb
+share/gromacs/top/encadv.ff/aminoacids.n.tdb
+share/gromacs/top/encadv.ff/aminoacids.r2b
+share/gromacs/top/encadv.ff/aminoacids.rtp
+share/gromacs/top/encadv.ff/atomtypes.atp
+share/gromacs/top/encadv.ff/ffbonded.itp
+share/gromacs/top/encadv.ff/ffnonbonded.itp
+share/gromacs/top/encadv.ff/forcefield.doc
+share/gromacs/top/encadv.ff/forcefield.itp
+share/gromacs/top/encadv.ff/watermodels.dat
 share/gromacs/top/export.dlg
-share/gromacs/top/f3c.itp
-share/gromacs/top/fa.itp
-share/gromacs/top/ffG43a1-c.tdb
-share/gromacs/top/ffG43a1-n.tdb
-share/gromacs/top/ffG43a1.atp
-share/gromacs/top/ffG43a1.ddb
-share/gromacs/top/ffG43a1.hdb
 share/gromacs/top/ffG43a1.itp
-share/gromacs/top/ffG43a1.rtp
-share/gromacs/top/ffG43a1bon.itp
-share/gromacs/top/ffG43a1nb.itp
-share/gromacs/top/ffG43a2-c.tdb
-share/gromacs/top/ffG43a2-n.tdb
-share/gromacs/top/ffG43a2.atp
-share/gromacs/top/ffG43a2.ddb
-share/gromacs/top/ffG43a2.hdb
 share/gromacs/top/ffG43a2.itp
-share/gromacs/top/ffG43a2.rtp
-share/gromacs/top/ffG43a2bon.itp
-share/gromacs/top/ffG43a2nb.itp
-share/gromacs/top/ffG45a3-c.tdb
-share/gromacs/top/ffG45a3-n.tdb
-share/gromacs/top/ffG45a3.atp
-share/gromacs/top/ffG45a3.ddb
-share/gromacs/top/ffG45a3.hdb
 share/gromacs/top/ffG45a3.itp
-share/gromacs/top/ffG45a3.rtp
-share/gromacs/top/ffG45a3bon.itp
-share/gromacs/top/ffG45a3nb.itp
-share/gromacs/top/ffG53a5-c.tdb
-share/gromacs/top/ffG53a5-n.tdb
-share/gromacs/top/ffG53a5.atp
-share/gromacs/top/ffG53a5.ddb
-share/gromacs/top/ffG53a5.hdb
 share/gromacs/top/ffG53a5.itp
-share/gromacs/top/ffG53a5.n2t
-share/gromacs/top/ffG53a5.rtp
-share/gromacs/top/ffG53a5bon.itp
-share/gromacs/top/ffG53a5nb.itp
-share/gromacs/top/ffG53a6-c.tdb
-share/gromacs/top/ffG53a6-n.tdb
-share/gromacs/top/ffG53a6.atp
-share/gromacs/top/ffG53a6.ddb
-share/gromacs/top/ffG53a6.hdb
 share/gromacs/top/ffG53a6.itp
-share/gromacs/top/ffG53a6.rtp
-share/gromacs/top/ffG53a6bon.itp
-share/gromacs/top/ffG53a6nb.itp
-share/gromacs/top/ff_dum.itp
-share/gromacs/top/ffencads-c.tdb
-share/gromacs/top/ffencads-n.tdb
-share/gromacs/top/ffencads.atp
-share/gromacs/top/ffencads.hdb
 share/gromacs/top/ffencads.itp
-share/gromacs/top/ffencads.rtp
-share/gromacs/top/ffencadsbon.itp
-share/gromacs/top/ffencadsnb.itp
-share/gromacs/top/ffencadv-c.tdb
-share/gromacs/top/ffencadv-n.tdb
-share/gromacs/top/ffencadv.atp
-share/gromacs/top/ffencadv.hdb
 share/gromacs/top/ffencadv.itp
-share/gromacs/top/ffencadv.rtp
-share/gromacs/top/ffencadvbon.itp
-share/gromacs/top/ffencadvnb.itp
-share/gromacs/top/ffgmx-c.tdb
-share/gromacs/top/ffgmx-n.tdb
-share/gromacs/top/ffgmx.atp
-share/gromacs/top/ffgmx.ddb
-share/gromacs/top/ffgmx.hdb
 share/gromacs/top/ffgmx.itp
-share/gromacs/top/ffgmx.rtp
-share/gromacs/top/ffgmx2-c.tdb
-share/gromacs/top/ffgmx2-n.tdb
-share/gromacs/top/ffgmx2.atp
-share/gromacs/top/ffgmx2.ddb
-share/gromacs/top/ffgmx2.hdb
 share/gromacs/top/ffgmx2.itp
-share/gromacs/top/ffgmx2.rtp
-share/gromacs/top/ffgmx2bon.itp
-share/gromacs/top/ffgmx2nb.itp
-share/gromacs/top/ffgmxbon.itp
-share/gromacs/top/ffgmxnb.itp
-share/gromacs/top/ffoplsaa-c.tdb
-share/gromacs/top/ffoplsaa-n.tdb
-share/gromacs/top/ffoplsaa.atp
-share/gromacs/top/ffoplsaa.ddb
-share/gromacs/top/ffoplsaa.hdb
+share/gromacs/top/ffoplsaa-n.tst
 share/gromacs/top/ffoplsaa.itp
-share/gromacs/top/ffoplsaa.n2t
-share/gromacs/top/ffoplsaa.rtp
-share/gromacs/top/ffoplsaabon.itp
-share/gromacs/top/ffoplsaanb.itp
 share/gromacs/top/flexspc.itp
 share/gromacs/top/flexspce.itp
 share/gromacs/top/flexwat-ferguson.itp
-share/gromacs/top/gromacs.dtd
+share/gromacs/top/gmx.ff/1mlg.itp
+share/gromacs/top/gmx.ff/2mlg.itp
+share/gromacs/top/gmx.ff/aminoacids.c.tdb
+share/gromacs/top/gmx.ff/aminoacids.hdb
+share/gromacs/top/gmx.ff/aminoacids.n.tdb
+share/gromacs/top/gmx.ff/aminoacids.rtp
+share/gromacs/top/gmx.ff/aminoacids.vsd
+share/gromacs/top/gmx.ff/atomtypes.atp
+share/gromacs/top/gmx.ff/decane.itp
+share/gromacs/top/gmx.ff/decane50.gro
+share/gromacs/top/gmx.ff/dlg.itp
+share/gromacs/top/gmx.ff/fa.itp
+share/gromacs/top/gmx.ff/ff_dum.itp
+share/gromacs/top/gmx.ff/ffbonded.itp
+share/gromacs/top/gmx.ff/ffnonbonded.itp
+share/gromacs/top/gmx.ff/forcefield.doc
+share/gromacs/top/gmx.ff/forcefield.itp
+share/gromacs/top/gmx.ff/h2p4o13.itp
+share/gromacs/top/gmx.ff/h2p8o25.itp
+share/gromacs/top/gmx.ff/h2po4.itp
+share/gromacs/top/gmx.ff/ions.itp
+share/gromacs/top/gmx.ff/spc.itp
+share/gromacs/top/gmx.ff/spce.itp
+share/gromacs/top/gmx.ff/tfe.itp
+share/gromacs/top/gmx.ff/tip3p.itp
+share/gromacs/top/gmx.ff/tip4p.itp
+share/gromacs/top/gmx.ff/watermodels.dat
+share/gromacs/top/gmx2.ff/aminoacids.c.tdb
+share/gromacs/top/gmx2.ff/aminoacids.hdb
+share/gromacs/top/gmx2.ff/aminoacids.n.tdb
+share/gromacs/top/gmx2.ff/aminoacids.rtp
+share/gromacs/top/gmx2.ff/aminoacids.vsd
+share/gromacs/top/gmx2.ff/atomtypes.atp
+share/gromacs/top/gmx2.ff/ff_dum.itp
+share/gromacs/top/gmx2.ff/ffbonded.itp
+share/gromacs/top/gmx2.ff/ffnonbonded.itp
+share/gromacs/top/gmx2.ff/forcefield.doc
+share/gromacs/top/gmx2.ff/forcefield.itp
+share/gromacs/top/gmx2.ff/ions.itp
+share/gromacs/top/gmx2.ff/spc.itp
+share/gromacs/top/gmx2.ff/spce.itp
+share/gromacs/top/gmx2.ff/tip3p.itp
+share/gromacs/top/gmx2.ff/tip4p.itp
+share/gromacs/top/gmx2.ff/watermodels.dat
+share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb
+share/gromacs/top/gromos43a1.ff/aminoacids.hdb
+share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb
+share/gromacs/top/gromos43a1.ff/aminoacids.r2b
+share/gromacs/top/gromos43a1.ff/aminoacids.rtp
+share/gromacs/top/gromos43a1.ff/aminoacids.vsd
+share/gromacs/top/gromos43a1.ff/atomtypes.atp
+share/gromacs/top/gromos43a1.ff/ff_dum.itp
+share/gromacs/top/gromos43a1.ff/ffbonded.itp
+share/gromacs/top/gromos43a1.ff/ffnonbonded.itp
+share/gromacs/top/gromos43a1.ff/forcefield.doc
+share/gromacs/top/gromos43a1.ff/forcefield.itp
+share/gromacs/top/gromos43a1.ff/ions.itp
+share/gromacs/top/gromos43a1.ff/methanol.itp
+share/gromacs/top/gromos43a1.ff/methanol216.gro
+share/gromacs/top/gromos43a1.ff/spc.itp
+share/gromacs/top/gromos43a1.ff/spce.itp
+share/gromacs/top/gromos43a1.ff/tip3p.itp
+share/gromacs/top/gromos43a1.ff/tip4p.itp
+share/gromacs/top/gromos43a1.ff/watermodels.dat
+share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb
+share/gromacs/top/gromos43a2.ff/aminoacids.hdb
+share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb
+share/gromacs/top/gromos43a2.ff/aminoacids.r2b
+share/gromacs/top/gromos43a2.ff/aminoacids.rtp
+share/gromacs/top/gromos43a2.ff/aminoacids.vsd
+share/gromacs/top/gromos43a2.ff/atomtypes.atp
+share/gromacs/top/gromos43a2.ff/ff_dum.itp
+share/gromacs/top/gromos43a2.ff/ffbonded.itp
+share/gromacs/top/gromos43a2.ff/ffnonbonded.itp
+share/gromacs/top/gromos43a2.ff/forcefield.doc
+share/gromacs/top/gromos43a2.ff/forcefield.itp
+share/gromacs/top/gromos43a2.ff/ions.itp
+share/gromacs/top/gromos43a2.ff/spc.itp
+share/gromacs/top/gromos43a2.ff/spce.itp
+share/gromacs/top/gromos43a2.ff/tip3p.itp
+share/gromacs/top/gromos43a2.ff/tip4p.itp
+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
diff --git a/biology/gromacs/distinfo b/biology/gromacs/distinfo
index 922dd4baa8a..4c16f573f8b 100644
--- a/biology/gromacs/distinfo
+++ b/biology/gromacs/distinfo
@@ -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
diff --git a/biology/gromacs/patches/patch-aa b/biology/gromacs/patches/patch-aa
index 13d6487d231..37e72b12be1 100644
--- a/biology/gromacs/patches/patch-aa
+++ b/biology/gromacs/patches/patch-aa
@@ -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.$(OBJEXT): gromacs
diff --git a/biology/gromacs/patches/patch-ab b/biology/gromacs/patches/patch-ab
deleted file mode 100644
index a25ab310a3c..00000000000
--- a/biology/gromacs/patches/patch-ab
+++ /dev/null
@@ -1,24 +0,0 @@
-$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 "$enable_software_sqrt" = "yes"; then
diff --git a/biology/gromacs/patches/patch-ac b/biology/gromacs/patches/patch-ac
deleted file mode 100644
index 534f950d288..00000000000
--- a/biology/gromacs/patches/patch-ac
+++ /dev/null
@@ -1,24 +0,0 @@
-$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 "$ppc_sqrt_niter" = "1"; then
-   GMX_POWERPC_SQRT_SINGLE_ITERATION_TRUE=
-   GMX_POWERPC_SQRT_SINGLE_ITERATION_FALSE='#'
- else
diff --git a/biology/gromacs/patches/patch-af b/biology/gromacs/patches/patch-af
deleted file mode 100644
index 502ad7e45b8..00000000000
--- a/biology/gromacs/patches/patch-af
+++ /dev/null
@@ -1,15 +0,0 @@
-$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 = $(libnb_kernel_ia32_3dnow_la_SOURCES)
diff --git a/biology/gromacs/patches/patch-ag b/biology/gromacs/patches/patch-ag
index 18d8bccb310..6c95daf96f7 100644
--- a/biology/gromacs/patches/patch-ag
+++ b/biology/gromacs/patches/patch-ag
@@ -1,11 +1,11 @@
-$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) $(LIBTOOLFLAGS) \
diff --git a/biology/gromacs/patches/patch-ah b/biology/gromacs/patches/patch-ah
index a123b39e06d..7584cd3acb7 100644
--- a/biology/gromacs/patches/patch-ah
+++ b/biology/gromacs/patches/patch-ah
@@ -1,11 +1,11 @@
-$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) $(LIBTOOLFLAGS) \
diff --git a/biology/gromacs/patches/patch-ak b/biology/gromacs/patches/patch-ak
deleted file mode 100644
index 3e98cf730fc..00000000000
--- a/biology/gromacs/patches/patch-ak
+++ /dev/null
@@ -1,34 +0,0 @@
-$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: