Import GROMACS 4.0.7 as biology/gromacs.

From pkgsrc-wip, packaged originally by Peter Ibsen Hansen.

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.

8 files changed, 821 insertions, 0 deletions

diff --git a/biology/gromacs/DESCR b/biology/gromacs/DESCR
new file mode 100644
index 00000000000..17d86649e93
--- /dev/null
+++ b/biology/gromacs/DESCR
@@ -0,0 +1,10 @@
+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,
+lipids and nucleic acids 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.
diff --git a/biology/gromacs/Makefile b/biology/gromacs/Makefile
new file mode 100644
index 00000000000..6a1c711d77e
--- /dev/null
+++ b/biology/gromacs/Makefile
@@ -0,0 +1,33 @@
+# $NetBSD: Makefile,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $
+#
+
+DISTNAME=		gromacs-4.0.7
+CATEGORIES=		biology
+MASTER_SITES=		ftp://ftp.gromacs.org/pub/gromacs/
+
+MAINTAINER=		pkgsrc-users@NetBSD.org
+HOMEPAGE=		http://www.gromacs.org/
+COMMENT=		Molecular dynamics package
+LICENSE=		gnu-gpl-v2
+
+PKG_DESTDIR_SUPPORT=	user-destdir
+
+# Official recommendation is not to use the gcc 4.1.x set of compilers.
+
+GNU_CONFIGURE=		yes
+USE_LIBTOOL=		yes
+USE_PKGLOCALEDIR=	yes
+
+CONFIGURE_ARGS+=	--enable-shared
+CONFIGURE_ARGS+=	--enable-double --program-suffix=
+CONFIGURE_ARGS+=	--with-gsl
+
+.include "options.mk"
+
+USE_TOOLS+=		perl:run
+REPLACE_PERL=		scripts/demux.pl scripts/xplor2gmx.pl
+
+.include "../../math/fftw/buildlink3.mk"
+.include "../../math/gsl/buildlink3.mk"	# optional
+.include "../../textproc/libxml2/buildlink3.mk"	# optional
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/gromacs/PLIST b/biology/gromacs/PLIST
new file mode 100644
index 00000000000..1eefe4bba92
--- /dev/null
+++ b/biology/gromacs/PLIST
@@ -0,0 +1,684 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $
+bin/GMXRC
+bin/GMXRC.bash
+bin/GMXRC.csh
+bin/GMXRC.zsh
+bin/anadock
+bin/completion.bash
+bin/completion.csh
+bin/completion.zsh
+bin/demux.pl
+bin/do_dssp
+bin/editconf
+bin/eneconv
+bin/g_anaeig
+bin/g_analyze
+bin/g_angle
+bin/g_bond
+bin/g_bundle
+bin/g_chi
+bin/g_cluster
+bin/g_clustsize
+bin/g_confrms
+bin/g_covar
+bin/g_current
+bin/g_density
+bin/g_densmap
+bin/g_dielectric
+bin/g_dih
+bin/g_dipoles
+bin/g_disre
+bin/g_dist
+bin/g_dyndom
+bin/g_enemat
+bin/g_energy
+bin/g_filter
+bin/g_gyrate
+bin/g_h2order
+bin/g_hbond
+bin/g_helix
+bin/g_helixorient
+bin/g_kinetics
+bin/g_lie
+bin/g_mdmat
+bin/g_mindist
+bin/g_morph
+bin/g_msd
+bin/g_nmeig
+bin/g_nmens
+bin/g_nmtraj
+bin/g_order
+bin/g_polystat
+bin/g_potential
+bin/g_principal
+bin/g_rama
+bin/g_rdf
+bin/g_rms
+bin/g_rmsdist
+bin/g_rmsf
+bin/g_rotacf
+bin/g_saltbr
+bin/g_sas
+bin/g_sdf
+bin/g_sgangle
+bin/g_sham
+bin/g_sorient
+bin/g_spatial
+bin/g_spol
+bin/g_tcaf
+bin/g_traj
+bin/g_vanhove
+bin/g_velacc
+bin/g_wham
+bin/genbox
+bin/genconf
+bin/genion
+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
+include/gromacs/bondf.h
+include/gromacs/calcgrid.h
+include/gromacs/calch.h
+include/gromacs/calcmu.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/disre.h
+include/gromacs/do_fit.h
+include/gromacs/domdec.h
+include/gromacs/domdec_network.h
+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/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_lapack.h
+include/gromacs/gmx_parallel_3dfft.h
+include/gromacs/gmx_random.h
+include/gromacs/gmx_system_xdr.h
+include/gromacs/gmx_thread.h
+include/gromacs/gmx_wallcycle.h
+include/gromacs/gmxcomplex.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/index.h
+include/gromacs/invblock.h
+include/gromacs/macros.h
+include/gromacs/magic.h
+include/gromacs/main.h
+include/gromacs/maths.h
+include/gromacs/matio.h
+include/gromacs/mdatoms.h
+include/gromacs/mdebin.h
+include/gromacs/mdrun.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/network.h
+include/gromacs/nonbonded.h
+include/gromacs/nrama.h
+include/gromacs/nrjac.h
+include/gromacs/nrnb.h
+include/gromacs/ns.h
+include/gromacs/nsgrid.h
+include/gromacs/orires.h
+include/gromacs/partdec.h
+include/gromacs/pbc.h
+include/gromacs/pdbio.h
+include/gromacs/pdebug.h
+include/gromacs/perf_est.h
+include/gromacs/physics.h
+include/gromacs/pme.h
+include/gromacs/pppm.h
+include/gromacs/princ.h
+include/gromacs/pull.h
+include/gromacs/qmmm.h
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+include/gromacs/rdgroup.h
+include/gromacs/readcomp.h
+include/gromacs/readinp.h
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+include/gromacs/rmpbc.h
+include/gromacs/shellfc.h
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+share/gromacs/top/decane.itp
+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/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.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/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/phbres.dat
+share/gromacs/top/ps.m2p
+share/gromacs/top/random.dat
+share/gromacs/top/refi_aa.dat
+share/gromacs/top/spc.itp
+share/gromacs/top/spc216.gro
+share/gromacs/top/spce.itp
+share/gromacs/top/specbond.dat
+share/gromacs/top/ss.map
+share/gromacs/top/surface.dat
+share/gromacs/top/sw.itp
+share/gromacs/top/table6-10.xvg
+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
+share/gromacs/tutor/gmxdemo/demo
+share/gromacs/tutor/methanol/conf.gro
+share/gromacs/tutor/methanol/grompp.mdp
+share/gromacs/tutor/methanol/index.ndx
+share/gromacs/tutor/methanol/methanol.itp
+share/gromacs/tutor/methanol/methanol.pdb
+share/gromacs/tutor/methanol/topol.top
+share/gromacs/tutor/mixed/conf.gro
+share/gromacs/tutor/mixed/grompp.mdp
+share/gromacs/tutor/mixed/index.ndx
+share/gromacs/tutor/mixed/mixed.pdb
+share/gromacs/tutor/mixed/topol.top
+share/gromacs/tutor/nmr1/conf.gro
+share/gromacs/tutor/nmr1/grompp.mdp
+share/gromacs/tutor/nmr1/pep.pdb
+share/gromacs/tutor/nmr1/topol.top
+share/gromacs/tutor/nmr2/conf.gro
+share/gromacs/tutor/nmr2/genconf.gcp
+share/gromacs/tutor/nmr2/grompp.mdp
+share/gromacs/tutor/nmr2/pep.pdb
+share/gromacs/tutor/nmr2/topol.top
+share/gromacs/tutor/speptide/em.mdp
+share/gromacs/tutor/speptide/full.mdp
+share/gromacs/tutor/speptide/pr.mdp
+share/gromacs/tutor/speptide/speptide.pdb
+share/gromacs/tutor/water/conf.gro
+share/gromacs/tutor/water/grompp.mdp
+share/gromacs/tutor/water/index.ndx
+share/gromacs/tutor/water/spc216.pdb
+share/gromacs/tutor/water/topol.top
diff --git a/biology/gromacs/distinfo b/biology/gromacs/distinfo
new file mode 100644
index 00000000000..39cee7939aa
--- /dev/null
+++ b/biology/gromacs/distinfo
@@ -0,0 +1,8 @@
+$NetBSD: distinfo,v 1.1.1.1 2010/03/15 14:08:49 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
diff --git a/biology/gromacs/options.mk b/biology/gromacs/options.mk
new file mode 100644
index 00000000000..55502741ee5
--- /dev/null
+++ b/biology/gromacs/options.mk
@@ -0,0 +1,19 @@
+# $NetBSD: options.mk,v 1.1.1.1 2010/03/15 14:08:49 asau Exp $
+
+PKG_OPTIONS_VAR=		PKG_OPTIONS.gromacs
+PKG_SUPPORTED_OPTIONS+=		x11
+PKG_SUGGESTED_OPTIONS+=		x11
+
+.include "../../mk/bsd.options.mk"
+
+PLIST_VARS=	x11
+
+# X support:
+.if !empty(PKG_OPTIONS:Mx11)
+CONFIGURE_ARGS+=	--with-x
+PLIST.x11=	yes
+
+.include "../../x11/libX11/buildlink3.mk"
+.include "../../x11/libICE/buildlink3.mk"
+.include "../../x11/libSM/buildlink3.mk"
+.endif
diff --git a/biology/gromacs/patches/patch-aa b/biology/gromacs/patches/patch-aa
new file mode 100644
index 00000000000..13d6487d231
--- /dev/null
+++ b/biology/gromacs/patches/patch-aa
@@ -0,0 +1,19 @@
+$NetBSD: patch-aa,v 1.1.1.1 2010/03/15 14:08:49 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 @@
+ 
+ Makefile.@host@ Makefile.@host@_double: Template.mak Makefile 
+ 	cat $(srcdir)/Template.mak | \
+-	sed 's,@LDFLAGS\@,$(LDFLAGS),' | \
+-	sed 's,@LIBS\@,$(LIBS),' | \
+-	sed 's,@CFLAGS\@,$(MYCFLAGS),' | \
++	sed 's|@LDFLAGS\@|$(LDFLAGS)|' | \
++	sed 's|@LIBS\@|$(LIBS)|' | \
++	sed 's|@CFLAGS\@|$(MYCFLAGS)|' | \
+ 	sed 's,@CC\@,$(CC),' | \
+ 	sed 's,@host\@,@host@,' >$@
+ # Tell versions [3.59,3.63) of GNU make to not export all variables.
diff --git a/biology/gromacs/patches/patch-ab b/biology/gromacs/patches/patch-ab
new file mode 100644
index 00000000000..a25ab310a3c
--- /dev/null
+++ b/biology/gromacs/patches/patch-ab
@@ -0,0 +1,24 @@
+$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 "$enable_software_sqrt" = "yes"; then
diff --git a/biology/gromacs/patches/patch-ac b/biology/gromacs/patches/patch-ac
new file mode 100644
index 00000000000..534f950d288
--- /dev/null
+++ b/biology/gromacs/patches/patch-ac
@@ -0,0 +1,24 @@
+$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