New port science/gromacs

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, and also the World's
fastest Molecular Dynamics under GPL.

PR:		71211
Submitted by:	Stephen Montgomery-Smith <stephen@math.missouri.edu>
Reviewed by:	Bruno Afonso <brunomiguel@dequim.ist.utl.pt>

5 files changed, 711 insertions, 0 deletions

diff --git a/science/Makefile b/science/Makefile
index b9dad676f674..ddd377bfde8d 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -23,6 +23,7 @@
     SUBDIR += ghemical
     SUBDIR += glens
     SUBDIR += gramps
+    SUBDIR += gromacs
     SUBDIR += hdf
     SUBDIR += hdf5
     SUBDIR += kmovisto
diff --git a/science/gromacs/Makefile b/science/gromacs/Makefile
new file mode 100644
index 000000000000..2bd5bb236961
--- /dev/null
+++ b/science/gromacs/Makefile
@@ -0,0 +1,150 @@
+# New ports collection makefile for: gromacs
+# Date created:		August 28 2004
+# Whom:			Stephen Montgomery-Smith <stephen@math.missouri.edu>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	gromacs
+PORTVERSION=	3.2.1
+CATEGORIES=	science
+MASTER_SITES=	ftp://ftp.gromacs.org/pub/gromacs/
+
+MAINTAINER=	stephen@math.missouri.edu
+COMMENT=	Compute molecular dynamics
+
+.ifndef WITHOUT_FFTW
+LIB_DEPENDS=	fftw:${PORTSDIR}/math/fftw:install
+.endif
+.ifdef WITH_MPI
+BUILD_DEPENDS=	${LOCALPREFIX}/mpich/bin/mpicc:${PORTSDIR}/net/mpich:install
+RUN_DEPENDS=	${LOCALPREFIX}/mpich/bin/mpicc:${PORTSDIR}/net/mpich:install
+.endif
+
+USE_GMAKE=	yes
+GNU_CONFIGURE=	yes
+CONFIGURE_TARGET=	--build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
+CONFIGURE_ENV=	CPPFLAGS=-I${LOCALBASE}/include LDFLAGS=-L${LOCALBASE}/lib
+CONFIGURE_ARGS=	--exec-prefix=${PREFIX}
+
+PLIST_SUB=	BUILD=${MACHINE_ARCH}-portbld-freebsd${OSREL}
+
+.ifndef WITHOUT_FFTW
+.ifdef WITH_FLOAT
+IGNORE= 	Cannot currently build with fftw and single precision floating point
+.elifdef WITH_MPI
+IGNORE= 	Cannot currently build with fftw and mpi support
+.endif
+.endif
+
+.ifdef WITHOUT_X
+PLIST_SUB+=	WITHOUT_X="@comment "
+CONFIGURE_ARGS+=	--without-x
+.else
+PLIST_SUB+=	WITHOUT_X=
+CONFIGURE_ARGS+=	--with-x
+USE_XLIB=	yes
+.endif
+
+.ifdef WITHOUT_FFTW
+CONFIGURE_ARGS+=	--without-fftw
+.endif
+
+.ifdef WITH_MPI
+CONFIGURE_ARGS+=	--enable-mpi
+CONFIGURE_ENV+=	MPICC=${PREFIX}/mpich/bin/mpicc
+PLIST_SUB+=	WITH_MPI= _MPI=_mpi
+.else
+PLIST_SUB+=	WITH_MPI="@comment " SUFFIX_MPI=
+.endif
+
+MAN1=	anadock.1 \
+	g_cluster.1 \
+	g_filter.1 \
+	g_potential.1 \
+	g_velacc.1 \
+	ngmx.1 \
+	cdist.1 \
+	g_clustsize.1 \
+	g_gyrate.1 \
+	g_rama.1 \
+	g_wham.1 \
+	pdb2gmx.1 \
+	disco.1 \
+	g_confrms.1 \
+	g_h2order.1 \
+	g_rdf.1 \
+	genbox.1 \
+	protonate.1 \
+	do_dssp.1 \
+	g_covar.1 \
+	g_hbond.1 \
+	g_rms.1 \
+	genconf.1 \
+	tpbconv.1 \
+	editconf.1 \
+	g_density.1 \
+	g_helix.1 \
+	g_rmsdist.1 \
+	genion.1 \
+	trjcat.1 \
+	eneconv.1 \
+	g_dielectric.1 \
+	g_lie.1 \
+	g_rmsf.1 \
+	genpr.1 \
+	trjconv.1 \
+	ffscan.1 \
+	g_dih.1 \
+	g_mdmat.1 \
+	g_rotacf.1 \
+	gmxcheck.1 \
+	trjorder.1 \
+	g_anaeig.1 \
+	g_dipoles.1 \
+	g_mindist.1 \
+	g_saltbr.1 \
+	gmxdump.1 \
+	wheel.1 \
+	g_analyze.1 \
+	g_disre.1 \
+	g_morph.1 \
+	g_sas.1 \
+	grompp.1 \
+	x2top.1 \
+	g_angle.1 \
+	g_dist.1 \
+	g_msd.1 \
+	g_sgangle.1 \
+	highway.1 \
+	xpm2ps.1 \
+	g_bond.1 \
+	g_dyndom.1 \
+	g_nmeig.1 \
+	g_sorient.1 \
+	make_ndx.1 \
+	xrama.1 \
+	g_bundle.1 \
+	g_enemat.1 \
+	g_nmens.1 \
+	g_tcaf.1 \
+	mdrun.1 \
+	g_chi.1 \
+	g_energy.1 \
+	g_order.1 \
+	g_traj.1 \
+	mk_angndx.1
+
+.include <bsd.port.pre.mk>
+
+pre-fetch:
+	@${ECHO}
+	@${ECHO} "OPTIONS:"
+	@${ECHO}
+	@${ECHO} "To compile without X11: define WITHOUT_X"
+	@${ECHO} "To compile using single precision floating point: define WITH_FLOAT"
+	@${ECHO} "To compile without fftw: define WITHOUT_FFTW"
+	@${ECHO} "To compile with mpi: define WITH_MPI"
+	@${ECHO}
+
+.include <bsd.port.post.mk>
diff --git a/science/gromacs/distinfo b/science/gromacs/distinfo
new file mode 100644
index 000000000000..c59371c50826
--- /dev/null
+++ b/science/gromacs/distinfo
@@ -0,0 +1,2 @@
+MD5 (gromacs-3.2.1.tar.gz) = d298386495f6ee39b3155ce951984485
+SIZE (gromacs-3.2.1.tar.gz) = 3302723
diff --git a/science/gromacs/pkg-descr b/science/gromacs/pkg-descr
new file mode 100644
index 000000000000..0193f6537b18
--- /dev/null
+++ b/science/gromacs/pkg-descr
@@ -0,0 +1,5 @@
+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.
+
+WWW: http://www.gromacs.org
diff --git a/science/gromacs/pkg-plist b/science/gromacs/pkg-plist
new file mode 100644
index 000000000000..8d8b3e0ef545
--- /dev/null
+++ b/science/gromacs/pkg-plist
@@ -0,0 +1,553 @@
+lib/libgmx%%SUFFIX_MPI%%.la
+lib/libgmx%%SUFFIX_MPI%%.a
+lib/libmd%%SUFFIX_MPI%%.la
+lib/libmd%%SUFFIX_MPI%%.a
+lib/libgmxana%%SUFFIX_MPI%%.la
+%%WITH_MPI%%lib/libgmxana%%SUFFIX_MPI%%.a
+lib/libgmxana.a
+%%WITHOUT_X%%bin/ngmx
+%%WITHOUT_X%%bin/xrama
+%%WITHOUT_X%%bin/highway
+bin/grompp
+bin/mdrun
+bin/tpbconv
+bin/pdb2gmx
+bin/protonate
+bin/luck
+bin/gmxdump
+bin/gmxcheck
+bin/x2top
+bin/ffscan
+bin/average
+bin/do_dssp
+bin/editconf
+bin/eneconv
+bin/genbox
+bin/genconf
+bin/genpr
+bin/make_ndx
+bin/mk_angndx
+bin/trjcat
+bin/trjconv
+bin/trjorder
+bin/wheel
+bin/xpm2ps
+bin/genion
+bin/anadock
+bin/cdist
+bin/disco
+bin/g_angle
+bin/make_edi
+bin/g_analyze
+bin/g_anaeig
+bin/g_bond
+bin/g_bundle
+bin/g_chi
+bin/g_cluster
+bin/g_confrms
+bin/g_covar
+bin/g_density
+bin/g_dih
+bin/g_dielectric
+bin/g_dipoles
+bin/g_disre
+bin/g_dist
+bin/g_dyndom
+bin/g_enemat
+bin/g_energy
+bin/g_lie
+bin/g_filter
+bin/g_gyrate
+bin/g_h2order
+bin/g_hbond
+bin/g_helix
+bin/g_mindist
+bin/g_msd
+bin/g_morph
+bin/g_nmeig
+bin/g_nmens
+bin/g_order
+bin/g_potential
+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_sgangle
+bin/g_sorient
+bin/g_tcaf
+bin/g_traj
+bin/g_velacc
+bin/g_clustsize
+bin/g_mdmat
+bin/g_wham
+bin/GMXRC
+bin/GMXRC.csh
+bin/GMXRC.bash
+bin/GMXRC.zsh
+bin/completion.csh
+bin/completion.bash
+bin/completion.zsh
+share/gromacs/top/ffgmx.itp
+share/gromacs/top/ffgmxnb.itp
+share/gromacs/top/ffgmxbon.itp
+share/gromacs/top/ffgmx.atp
+share/gromacs/top/ffgmx.hdb
+share/gromacs/top/ffgmx.n2t
+share/gromacs/top/ffgmx.rtp
+share/gromacs/top/ffgmx-c.tdb
+share/gromacs/top/ffgmx-n.tdb
+share/gromacs/top/ffgmx2.itp
+share/gromacs/top/ffgmx2nb.itp
+share/gromacs/top/ffgmx2bon.itp
+share/gromacs/top/ffgmx2.atp
+share/gromacs/top/ffgmx2.hdb
+share/gromacs/top/ffgmx2.rtp
+share/gromacs/top/ffgmx2-c.tdb
+share/gromacs/top/ffgmx2-n.tdb
+share/gromacs/top/ffG43a1.itp
+share/gromacs/top/ffG43a1nb.itp
+share/gromacs/top/ffG43a1bon.itp
+share/gromacs/top/ffG43a1.atp
+share/gromacs/top/ffG43a1.hdb
+share/gromacs/top/ffG43a1.rtp
+share/gromacs/top/ffG43a1-c.tdb
+share/gromacs/top/ffG43a1-n.tdb
+share/gromacs/top/ffG43a2.itp
+share/gromacs/top/ffG43a2nb.itp
+share/gromacs/top/ffG43a2bon.itp
+share/gromacs/top/ffG43a2.atp
+share/gromacs/top/ffG43a2.hdb
+share/gromacs/top/ffG43a2.rtp
+share/gromacs/top/ffG43a2-c.tdb
+share/gromacs/top/ffG43a2-n.tdb
+share/gromacs/top/ffG43b1.itp
+share/gromacs/top/ffG43b1nb.itp
+share/gromacs/top/ffG43b1bon.itp
+share/gromacs/top/ffG43b1.atp
+share/gromacs/top/ffG43b1.hdb
+share/gromacs/top/ffG43b1.rtp
+share/gromacs/top/ffG43b1-c.tdb
+share/gromacs/top/ffG43b1-n.tdb
+share/gromacs/top/ffgmx.ddb
+share/gromacs/top/ffgmx2.ddb
+share/gromacs/top/ffG43a1.ddb
+share/gromacs/top/ffG43a2.ddb
+share/gromacs/top/ffG43b1.ddb
+share/gromacs/top/ffoplsaa.atp
+share/gromacs/top/ffoplsaa.itp
+share/gromacs/top/ffoplsaabon.itp
+share/gromacs/top/ffoplsaanb.itp
+share/gromacs/top/ffoplsaa.hdb
+share/gromacs/top/ffoplsaa-n.tdb
+share/gromacs/top/ffoplsaa-c.tdb
+share/gromacs/top/ffoplsaa.rtp
+share/gromacs/top/ffoplsaa.ddb
+share/gromacs/top/1mlg.itp
+share/gromacs/top/2mlg.itp
+share/gromacs/top/benzamide.itp
+share/gromacs/top/bondadd.itp
+share/gromacs/top/buck.itp
+share/gromacs/top/decane.itp
+share/gromacs/top/dlg.itp
+share/gromacs/top/dmso.itp
+share/gromacs/top/fa.itp
+share/gromacs/top/ff_dum.itp
+share/gromacs/top/flexspc.itp
+share/gromacs/top/flexspce.itp
+share/gromacs/top/flexwat-ferguson.itp
+share/gromacs/top/h2p4o13.itp
+share/gromacs/top/h2p8o25.itp
+share/gromacs/top/h2po4.itp
+share/gromacs/top/ions.itp
+share/gromacs/top/methanol.itp
+share/gromacs/top/spc.itp
+share/gromacs/top/spce.itp
+share/gromacs/top/tfe.itp
+share/gromacs/top/tip3p.itp
+share/gromacs/top/tip4p.itp
+share/gromacs/top/urea.itp
+share/gromacs/top/dgsolv.dat
+share/gromacs/top/dec50.gro
+share/gromacs/top/dmso.gro
+share/gromacs/top/spc216.gro
+share/gromacs/top/tip4p.gro
+share/gromacs/top/urea+h2o.gro
+share/gromacs/top/aminoacids.dat
+share/gromacs/top/atommass.dat
+share/gromacs/top/bromacs.dat
+share/gromacs/top/ca-shift.dat
+share/gromacs/top/cb-shift.dat
+share/gromacs/top/co-shift.dat
+share/gromacs/top/edissoc.dat
+share/gromacs/top/FF.dat
+share/gromacs/top/ss.map
+share/gromacs/top/gurgle.dat
+share/gromacs/top/ha-shift.dat
+share/gromacs/top/links.dat
+share/gromacs/top/phbres.dat
+share/gromacs/top/random.dat
+share/gromacs/top/refi_aa.dat
+share/gromacs/top/specbond.dat
+share/gromacs/top/surface.dat
+share/gromacs/top/vdwradii.dat
+share/gromacs/top/xlateat.dat
+share/gromacs/top/export.dlg
+share/gromacs/top/bonds.dlg
+share/gromacs/top/ps.m2p
+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/atom_nom.tbl
+share/gromacs/top/gromacs.dtd
+share/gromacs/top/tip5p.gro
+share/gromacs/top/tip5p.itp
+share/gromacs/top/sw.itp
+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/index.ndx
+share/gromacs/tutor/water/conf.gro
+share/gromacs/tutor/water/spc216.pdb
+share/gromacs/tutor/water/grompp.mdp
+share/gromacs/tutor/water/topol.top
+share/gromacs/tutor/gmxdemo/cpeptide.pdb
+share/gromacs/tutor/gmxdemo/demo
+share/gromacs/tutor/methanol/index.ndx
+share/gromacs/tutor/methanol/conf.gro
+share/gromacs/tutor/methanol/methanol.pdb
+share/gromacs/tutor/methanol/grompp.mdp
+share/gromacs/tutor/methanol/topol.top
+share/gromacs/tutor/methanol/methanol.itp
+share/gromacs/tutor/mixed/index.ndx
+share/gromacs/tutor/mixed/conf.gro
+share/gromacs/tutor/mixed/mixed.pdb
+share/gromacs/tutor/mixed/grompp.mdp
+share/gromacs/tutor/mixed/topol.top
+share/gromacs/tutor/cleanit
+share/gromacs/template/template.c
+share/gromacs/template/README
+share/gromacs/template/Makefile.%%BUILD%%
+share/gromacs/html/online.html
+share/gromacs/html/gmxfaq.html
+share/gromacs/html/images/features.gif
+share/gromacs/html/images/flow_leftrightup.gif
+share/gromacs/html/images/flow_vrule.gif
+share/gromacs/html/images/flow_down.gif
+share/gromacs/html/images/flow_leftup.gif
+share/gromacs/html/images/links.gif
+share/gromacs/html/images/articles.gif
+share/gromacs/html/images/flow_downleft.gif
+share/gromacs/html/images/flow_right+left.gif
+share/gromacs/html/images/mail.gif
+share/gromacs/html/images/bench.gif
+share/gromacs/html/images/flow_hline.gif
+share/gromacs/html/images/flow_right.gif
+share/gromacs/html/images/manual.gif
+share/gromacs/html/images/charts_down.gif
+share/gromacs/html/images/flow_left.gif
+share/gromacs/html/images/flow_rightleftdown.gif
+share/gromacs/html/images/gmxlogo_small.jpg
+share/gromacs/html/images/charts_up.gif
+share/gromacs/html/images/faq.gif
+share/gromacs/html/images/flow_leftright.gif
+share/gromacs/html/images/flow_uprightleft.gif
+share/gromacs/html/images/software.gif
+share/gromacs/html/images/flow_leftrightdown.gif
+share/gromacs/html/images/flow_vline.gif
+share/gromacs/html/images/topologies.gif
+share/gromacs/html/images/plotje.gif
+share/gromacs/html/images/xvgr.gif
+share/gromacs/html/images/1ctf-0.jpg
+share/gromacs/html/images/1ctf-0.2.jpg
+share/gromacs/html/images/1ctf-0.5.jpg
+share/gromacs/html/images/1ctf-1.jpg
+share/gromacs/html/images/1ctf-4.jpg
+share/gromacs/html/images/1ctf-10.jpg
+share/gromacs/html/online/dat.html
+share/gromacs/html/online/g_disre.html
+share/gromacs/html/online/g_sorient.html
+share/gromacs/html/online/ndx.html
+share/gromacs/html/online/dlg.html
+share/gromacs/html/online/g_dist.html
+share/gromacs/html/online/g_tcaf.html
+share/gromacs/html/online/ngmx.html
+share/gromacs/html/online/do_dssp.html
+share/gromacs/html/online/g_dyndom.html
+share/gromacs/html/online/g_traj.html
+share/gromacs/html/online/edi.html
+share/gromacs/html/online/g_enemat.html
+share/gromacs/html/online/g_velacc.html
+share/gromacs/html/online/options.html
+share/gromacs/html/online/editconf.html
+share/gromacs/html/online/g_energy.html
+share/gromacs/html/online/genbox.html
+share/gromacs/html/online/out.html
+share/gromacs/html/online/edo.html
+share/gromacs/html/online/g_gyrate.html
+share/gromacs/html/online/genconf.html
+share/gromacs/html/online/pdb.html
+share/gromacs/html/online/edr.html
+share/gromacs/html/online/g_h2order.html
+share/gromacs/html/online/genion.html
+share/gromacs/html/online/pdb2gmx.html
+share/gromacs/html/online/ene.html
+share/gromacs/html/online/g_hbond.html
+share/gromacs/html/online/genpr.html
+share/gromacs/html/online/protonate.html
+share/gromacs/html/online/eneconv.html
+share/gromacs/html/online/g_helix.html
+share/gromacs/html/online/getting_started.html
+share/gromacs/html/online/rtp.html
+share/gromacs/html/online/eps.html
+share/gromacs/html/online/g_lie.html
+share/gromacs/html/online/gmxcheck.html
+share/gromacs/html/online/tex.html
+share/gromacs/html/online/files.html
+share/gromacs/html/online/g_mdmat.html
+share/gromacs/html/online/gmxdump.html
+share/gromacs/html/online/top.html
+share/gromacs/html/online/flow.html
+share/gromacs/html/online/g_mindist.html
+share/gromacs/html/online/gro.html
+share/gromacs/html/online/tpa.html
+share/gromacs/html/online/g87.html
+share/gromacs/html/online/g_morph.html
+share/gromacs/html/online/grompp.html
+share/gromacs/html/online/tpb.html
+share/gromacs/html/online/g96.html
+share/gromacs/html/online/g_msd.html
+share/gromacs/html/online/hat.html
+share/gromacs/html/online/tpbconv.html
+share/gromacs/html/online/g_anaeig.html
+share/gromacs/html/online/g_nmeig.html
+share/gromacs/html/online/highway.html
+share/gromacs/html/online/tpr.html
+share/gromacs/html/online/g_analyze.html
+share/gromacs/html/online/g_nmens.html
+share/gromacs/html/online/include_bot.html
+share/gromacs/html/online/trj.html
+share/gromacs/html/online/g_angle.html
+share/gromacs/html/online/g_order.html
+share/gromacs/html/online/include_top.html
+share/gromacs/html/online/trjcat.html
+share/gromacs/html/online/g_bond.html
+share/gromacs/html/online/g_potential.html
+share/gromacs/html/online/itp.html
+share/gromacs/html/online/trjconv.html
+share/gromacs/html/online/g_bundle.html
+share/gromacs/html/online/g_rama.html
+share/gromacs/html/online/log.html
+share/gromacs/html/online/trjorder.html
+share/gromacs/html/online/g_chi.html
+share/gromacs/html/online/g_rdf.html
+share/gromacs/html/online/m2p.html
+share/gromacs/html/online/trr.html
+share/gromacs/html/online/g_cluster.html
+share/gromacs/html/online/g_rms.html
+share/gromacs/html/online/make_ndx.html
+share/gromacs/html/online/wheel.html
+share/gromacs/html/online/g_confrms.html
+share/gromacs/html/online/g_rmsdist.html
+share/gromacs/html/online/map.html
+share/gromacs/html/online/x2top.html
+share/gromacs/html/online/g_covar.html
+share/gromacs/html/online/g_rmsf.html
+share/gromacs/html/online/mdp.html
+share/gromacs/html/online/xpm.html
+share/gromacs/html/online/g_density.html
+share/gromacs/html/online/g_rotacf.html
+share/gromacs/html/online/mdp_opt.html
+share/gromacs/html/online/xpm2ps.html
+share/gromacs/html/online/g_dielectric.html
+share/gromacs/html/online/g_saltbr.html
+share/gromacs/html/online/mdrun.html
+share/gromacs/html/online/xrama.html
+share/gromacs/html/online/g_dih.html
+share/gromacs/html/online/g_sas.html
+share/gromacs/html/online/mk_angndx.html
+share/gromacs/html/online/xtc.html
+share/gromacs/html/online/g_dipoles.html
+share/gromacs/html/online/g_sgangle.html
+share/gromacs/html/online/mtx.html
+share/gromacs/html/online/xvg.html
+share/gromacs/html/online/style.css
+share/gromacs/html/online/water.html
+share/gromacs/html/online/gmxdemo.html
+share/gromacs/html/online/speptide.html
+share/gromacs/html/online/yourown.html
+share/gromacs/html/online/methanol.html
+share/gromacs/html/online/mixed.html
+share/gromacs/html/online/protunf.html
+include/gromacs/3dview.h
+include/gromacs/do_md.h
+include/gromacs/invblock.h
+include/gromacs/nrjac.h
+include/gromacs/tpxio.h
+include/gromacs/assert.h
+include/gromacs/dihre.h
+include/gromacs/nrnb.h
+include/gromacs/sheader.h
+include/gromacs/transfer.h
+include/gromacs/atomprop.h
+include/gromacs/dummies.h
+include/gromacs/ns.h
+include/gromacs/shift.h
+include/gromacs/trnio.h
+include/gromacs/axp_asm.h
+include/gromacs/ebin.h
+include/gromacs/macros.h
+include/gromacs/nsb.h
+include/gromacs/shift_util.h
+include/gromacs/txtdump.h
+include/gromacs/edsam.h
+include/gromacs/magic.h
+include/gromacs/nsgrid.h
+include/gromacs/typedefs.h
+include/gromacs/block_tx.h
+include/gromacs/enxio.h
+include/gromacs/main.h
+include/gromacs/pbc.h
+include/gromacs/smalloc.h
+include/gromacs/update.h
+include/gromacs/bondf.h
+include/gromacs/ewald.h
+include/gromacs/maths.h
+include/gromacs/pdbio.h
+include/gromacs/sortwater.h
+include/gromacs/utils.h
+include/gromacs/ewald_util.h
+include/gromacs/matio.h
+include/gromacs/pdebug.h
+include/gromacs/split.h
+include/gromacs/vcm.h
+include/gromacs/calcgrid.h
+include/gromacs/fatal.h
+include/gromacs/mdatoms.h
+include/gromacs/physics.h
+include/gromacs/vec.h
+include/gromacs/calch.h
+include/gromacs/ffscanf.h
+include/gromacs/mdebin.h
+include/gromacs/pme.h
+include/gromacs/statusio.h
+include/gromacs/viewit.h
+include/gromacs/calcmu.h
+include/gromacs/fftgrid.h
+include/gromacs/mdrun.h
+include/gromacs/pppm.h
+include/gromacs/statutil.h
+include/gromacs/callf77.h
+include/gromacs/fftw_wrapper.h
+include/gromacs/gmx_ana.h
+include/gromacs/princ.h
+include/gromacs/wgms.h
+include/gromacs/gmx_system_xdr.h
+include/gromacs/filenm.h
+include/gromacs/pull.h
+include/gromacs/rdgroup.h
+include/gromacs/strdb.h
+include/gromacs/wman.h
+include/gromacs/force.h
+include/gromacs/string2.h
+include/gromacs/writeps.h
+include/gromacs/gmxcomplex.h
+include/gromacs/futil.h
+include/gromacs/metacode.h
+include/gromacs/random.h
+include/gromacs/struc2.h
+include/gromacs/x86_3dnow.h
+include/gromacs/gbutil.h
+include/gromacs/gmx_random.h
+include/gromacs/rbin.h
+include/gromacs/detectcpu.h
+include/gromacs/tgroup.h
+include/gromacs/mshift.h
+include/gromacs/symtab.h
+include/gromacs/x86_sse.h
+include/gromacs/confio.h
+include/gromacs/gmxfio.h
+include/gromacs/xdrf.h
+include/gromacs/constr.h
+include/gromacs/grompp.h
+include/gromacs/names.h
+include/gromacs/readcomp.h
+include/gromacs/xtcio.h
+include/gromacs/copyrite.h
+include/gromacs/gstat.h
+include/gromacs/network.h
+include/gromacs/readinp.h
+include/gromacs/sysstuff.h
+include/gromacs/xvgr.h
+include/gromacs/index.h
+include/gromacs/mvdata.h
+include/gromacs/disre.h
+include/gromacs/orires.h
+include/gromacs/x86_sse2.h
+include/gromacs/init.h
+include/gromacs/nr.h
+include/gromacs/reorder.h
+include/gromacs/tags.h
+include/gromacs/do_fit.h
+include/gromacs/nrama.h
+include/gromacs/rmpbc.h
+include/gromacs/ppc_altivec.h
+include/gromacs/types/atoms.h
+include/gromacs/types/edsams.h
+include/gromacs/types/forcerec.h
+include/gromacs/types/ifunc.h
+include/gromacs/types/mdatom.h
+include/gromacs/types/nsborder.h
+include/gromacs/types/simple.h
+include/gromacs/types/block.h
+include/gromacs/types/energy.h
+include/gromacs/types/graph.h
+include/gromacs/types/inputrec.h
+include/gromacs/types/nblist.h
+include/gromacs/types/nsgrid.h
+include/gromacs/types/symtab.h
+include/gromacs/types/commrec.h
+include/gromacs/types/enums.h
+include/gromacs/types/group.h
+include/gromacs/types/ishift.h
+include/gromacs/types/nbslist.h
+include/gromacs/types/parm.h
+include/gromacs/types/topology.h
+include/gromacs/types/fcdata.h
+include/gromacs/types/filenm.h
+include/gromacs/types/idef.h
+include/gromacs/types/matrix.h
+include/gromacs/types/nrnb.h
+include/gromacs/types/trx.h
+include/gromacs/types/state.h
+@dirrm share/gromacs/tutor/water
+@dirrm share/gromacs/tutor/speptide
+@dirrm share/gromacs/tutor/nmr2
+@dirrm share/gromacs/tutor/nmr1
+@dirrm share/gromacs/tutor/mixed
+@dirrm share/gromacs/tutor/methanol
+@dirrm share/gromacs/tutor/gmxdemo
+@dirrm share/gromacs/tutor
+@dirrm share/gromacs/top
+@dirrm share/gromacs/template
+@dirrm share/gromacs/html/online
+@dirrm share/gromacs/html/images
+@dirrm share/gromacs/html
+@dirrm share/gromacs
+@dirrm include/gromacs/types
+@dirrm include/gromacs