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.

3 files changed, 25 insertions, 8 deletions

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