From 7eece3338be4cebce73da6524ff697994298dc17 Mon Sep 17 00:00:00 2001 From: asau Date: Sat, 14 Jan 2012 00:38:18 +0000 Subject: Update to Gromacs 4.5.5 Notable changes in Gromacs 4.5.5: * Improved pdb2gmx -chainsep option and reintroduced the -merge option. * Fixed mdrun file appending truncating files to 0 bytes when continuation runs stopped before writing new output. * Fixed COM pulling with multiple constraints checking the convergence of one constraint instead of all. * Fixed some dihedrals in sugars in Gromos53a5/6 working on the wrong atoms. * AmberGS force field is now based on Amber94 instead of Amber96. * Moved hydrogens in Charmm27 protein termini to separate charge groups and added ACE and CT3 residue types. * Many small fixes which avoid termination with fatal errors or crashes in mdrun and tools. * Many small updates to the manual pages of programs. --- biology/gromacs/Makefile | 10 ++++++++-- biology/gromacs/PLIST | 15 +++++++++++++-- biology/gromacs/distinfo | 8 ++++---- 3 files changed, 25 insertions(+), 8 deletions(-) (limited to 'biology/gromacs') diff --git a/biology/gromacs/Makefile b/biology/gromacs/Makefile index a2a8099a92a..210d6f1b23f 100644 --- a/biology/gromacs/Makefile +++ b/biology/gromacs/Makefile @@ -1,7 +1,7 @@ -# $NetBSD: Makefile,v 1.7 2011/03/23 05:36:29 asau Exp $ +# $NetBSD: Makefile,v 1.8 2012/01/14 00:38:18 asau Exp $ # -DISTNAME= gromacs-4.5.4 +DISTNAME= gromacs-4.5.5 CATEGORIES= biology MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/ @@ -29,6 +29,12 @@ CONFIGURE_ARGS+= --disable-gcc41-check USE_TOOLS+= perl:run REPLACE_PERL= scripts/demux.pl scripts/xplor2gmx.pl +.include "../../mk/bsd.prefs.mk" + +.if $(MACHINE_ARCH) == "i386" +CFLAGS+= -msse -msse2 +.endif + .include "../../math/fftw/buildlink3.mk" .include "../../math/gsl/buildlink3.mk" # optional .include "../../textproc/libxml2/buildlink3.mk" # optional diff --git a/biology/gromacs/PLIST b/biology/gromacs/PLIST index 1351f4b4616..a52b6f695bf 100644 --- a/biology/gromacs/PLIST +++ b/biology/gromacs/PLIST @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.6 2011/03/23 05:36:29 asau Exp $ +@comment $NetBSD: PLIST,v 1.7 2012/01/14 00:38:18 asau Exp $ bin/GMXRC bin/GMXRC.bash bin/GMXRC.csh @@ -25,11 +25,13 @@ bin/g_covar bin/g_current bin/g_density bin/g_densmap +bin/g_densorder bin/g_dielectric bin/g_dih bin/g_dipoles bin/g_disre bin/g_dist +bin/g_dos bin/g_dyndom bin/g_enemat bin/g_energy @@ -39,6 +41,7 @@ bin/g_h2order bin/g_hbond bin/g_helix bin/g_helixorient +bin/g_hydorder bin/g_kinetics bin/g_lie bin/g_luck @@ -240,10 +243,10 @@ 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/numa_malloc.h include/gromacs/thread_mpi/threads.h include/gromacs/thread_mpi/tmpi.h include/gromacs/thread_mpi/wait.h @@ -265,15 +268,18 @@ include/gromacs/types/fcdata.h include/gromacs/types/filenm.h include/gromacs/types/forcerec.h include/gromacs/types/genborn.h +include/gromacs/types/globsig.h include/gromacs/types/graph.h include/gromacs/types/group.h include/gromacs/types/idef.h include/gromacs/types/ifunc.h include/gromacs/types/inputrec.h include/gromacs/types/ishift.h +include/gromacs/types/iteratedconstraints.h include/gromacs/types/matrix.h include/gromacs/types/mdatom.h include/gromacs/types/nblist.h +include/gromacs/types/nlistheuristics.h include/gromacs/types/nrnb.h include/gromacs/types/ns.h include/gromacs/types/nsgrid.h @@ -327,6 +333,7 @@ man/man1/g_covar.1 man/man1/g_current.1 man/man1/g_density.1 man/man1/g_densmap.1 +man/man1/g_densorder.1 man/man1/g_dielectric.1 man/man1/g_dih.1 man/man1/g_dipoles.1 @@ -341,6 +348,7 @@ man/man1/g_h2order.1 man/man1/g_hbond.1 man/man1/g_helix.1 man/man1/g_helixorient.1 +man/man1/g_hydorder.1 man/man1/g_lie.1 man/man1/g_mdmat.1 man/man1/g_membed.1 @@ -350,7 +358,9 @@ man/man1/g_msd.1 man/man1/g_nmeig.1 man/man1/g_nmens.1 man/man1/g_nmtraj.1 +man/man1/g_options.1 man/man1/g_order.1 +man/man1/g_pme_error.1 man/man1/g_polystat.1 man/man1/g_potential.1 man/man1/g_principal.1 @@ -461,6 +471,7 @@ share/gromacs/html/online/g_confrms.html share/gromacs/html/online/g_covar.html share/gromacs/html/online/g_density.html share/gromacs/html/online/g_densmap.html +share/gromacs/html/online/g_densorder.html share/gromacs/html/online/g_dielectric.html share/gromacs/html/online/g_dih.html share/gromacs/html/online/g_dipoles.html diff --git a/biology/gromacs/distinfo b/biology/gromacs/distinfo index e19cc90a948..d7ebbece748 100644 --- a/biology/gromacs/distinfo +++ b/biology/gromacs/distinfo @@ -1,8 +1,8 @@ -$NetBSD: distinfo,v 1.8 2011/03/23 05:36:29 asau Exp $ +$NetBSD: distinfo,v 1.9 2012/01/14 00:38:18 asau Exp $ -SHA1 (gromacs-4.5.4.tar.gz) = c7b3fbd2f3ddf915bc082e7effe76a8276563726 -RMD160 (gromacs-4.5.4.tar.gz) = 96065d1a173231f75869764a08eb4feccc1ec597 -Size (gromacs-4.5.4.tar.gz) = 10353984 bytes +SHA1 (gromacs-4.5.5.tar.gz) = ce4b4f9a0453dd2ffea72f28ea0bc7bb7a72f479 +RMD160 (gromacs-4.5.5.tar.gz) = a3d40c3ac6ec9ee3e4607bd35afca1dd4715154e +Size (gromacs-4.5.5.tar.gz) = 10398178 bytes SHA1 (patch-aa) = 29c6683c71989621f0f41682b1c225f524a2d84f SHA1 (patch-ad) = 68b37154ba466e28cad0e539e25253c901421aaa SHA1 (patch-ae) = 59a5e88abeee883483b557cab1681c9a9098870f -- cgit v1.2.3