Commit 252e4b48 authored by Nicholas Breen's avatar Nicholas Breen

New upstream relese; update GPU rules

parent 4ec466ee
gromacs (5.0.2-1) unstable; urgency=medium
* New upstream release.
* Update Standards-Version to 3.9.6, no changes required.
* Update rules to build GPU-accelerated packages, with thanks to
Steffen Möller.
-- Nicholas Breen <nbreen@debian.org> Sun, 05 Oct 2014 10:29:34 -0700
gromacs (5.0.1-1) unstable; urgency=medium
* New upstream release.
......
......@@ -4,7 +4,7 @@ Priority: extra
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders: Nicholas Breen <nbreen@debian.org>
Build-Depends: debhelper (>= 7.0.0), libfftw3-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.2.4-5) [alpha amd64 arm64 armel armhf hurd-i386 i386 ia64 kfreebsd-amd64 kfreebsd-i386 mips mips64 mips64el mipsel powerpc powerpcspe ppc64 ppc64el sparc sparc64], libx11-dev, zlib1g-dev, libgsl0-dev, libxml2-dev, libblas-dev, liblapack-dev, libboost-dev, cmake
Standards-Version: 3.9.5
Standards-Version: 3.9.6
Homepage: http://www.gromacs.org/
Vcs-Browser: http://anonscm.debian.org/viewvc/debichem/
Vcs-Svn: svn://anonscm.debian.org/debichem/unstable/gromacs/
......
......@@ -11,7 +11,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-anadock.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-anadock.1
+++ gromacs-5.0.1/docs/man/man1/gmx-anadock.1
@@ -1,11 +1,11 @@
.TH gmx-anadock 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-anadock 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-anadock - Cluster structures from Autodock runs
+gmx-anadock \- Cluster structures from Autodock runs
......@@ -31,7 +31,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-anaeig.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-anaeig.1
+++ gromacs-5.0.1/docs/man/man1/gmx-anaeig.1
@@ -1,19 +1,19 @@
.TH gmx-anaeig 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-anaeig 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-anaeig - Analyze eigenvectors/normal modes
+gmx-anaeig \- Analyze eigenvectors/normal modes
......@@ -67,7 +67,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-analyze.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-analyze.1
+++ gromacs-5.0.1/docs/man/man1/gmx-analyze.1
@@ -1,19 +1,19 @@
.TH gmx-analyze 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-analyze 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-analyze - Analyze data sets
+gmx-analyze \- Analyze data sets
......@@ -103,7 +103,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-angle.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-angle.1
+++ gromacs-5.0.1/docs/man/man1/gmx-angle.1
@@ -1,16 +1,16 @@
.TH gmx-angle 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-angle 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-angle - Calculate distributions and correlations for angles and dihedrals
+gmx-angle \- Calculate distributions and correlations for angles and dihedrals
......@@ -133,7 +133,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-bar.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-bar.1
+++ gromacs-5.0.1/docs/man/man1/gmx-bar.1
@@ -1,13 +1,13 @@
.TH gmx-bar 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-bar 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-bar - Calculate free energy difference estimates through Bennett's acceptance ratio
+gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio
......@@ -157,7 +157,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-bundle.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-bundle.1
+++ gromacs-5.0.1/docs/man/man1/gmx-bundle.1
@@ -1,15 +1,15 @@
.TH gmx-bundle 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-bundle 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-bundle - Analyze bundles of axes, e.g., helices
+gmx-bundle \- Analyze bundles of axes, e.g., helices
......@@ -185,7 +185,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-check.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-check.1
+++ gromacs-5.0.1/docs/man/man1/gmx-check.1
@@ -1,14 +1,14 @@
.TH gmx-check 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-check 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-check - Check and compare files
+gmx-check \- Check and compare files
......@@ -211,7 +211,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-chi.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-chi.1
+++ gromacs-5.0.1/docs/man/man1/gmx-chi.1
@@ -1,20 +1,20 @@
.TH gmx-chi 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-chi 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-chi - Calculate everything you want to know about chi and other dihedrals
+gmx-chi \- Calculate everything you want to know about chi and other dihedrals
......@@ -249,7 +249,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-cluster.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-cluster.1
+++ gromacs-5.0.1/docs/man/man1/gmx-cluster.1
@@ -1,21 +1,21 @@
.TH gmx-cluster 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-cluster 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-cluster - Cluster structures
+gmx-cluster \- Cluster structures
......@@ -289,7 +289,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-clustsize.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-clustsize.1
+++ gromacs-5.0.1/docs/man/man1/gmx-clustsize.1
@@ -1,16 +1,16 @@
.TH gmx-clustsize 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-clustsize 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-clustsize - Calculate size distributions of atomic clusters
+gmx-clustsize \- Calculate size distributions of atomic clusters
......@@ -319,7 +319,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-confrms.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-confrms.1
+++ gromacs-5.0.1/docs/man/man1/gmx-confrms.1
@@ -1,13 +1,13 @@
.TH gmx-confrms 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-confrms 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-confrms - Fit two structures and calculates the RMSD
+gmx-confrms \- Fit two structures and calculates the RMSD
......@@ -343,7 +343,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-convert-tpr.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-convert-tpr.1
+++ gromacs-5.0.1/docs/man/man1/gmx-convert-tpr.1
@@ -1,13 +1,13 @@
.TH gmx-convert-tpr 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-convert-tpr 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-convert-tpr - Make a modifed run-input file
+gmx-convert-tpr \- Make a modifed run-input file
......@@ -367,7 +367,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-covar.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-covar.1
+++ gromacs-5.0.1/docs/man/man1/gmx-covar.1
@@ -1,14 +1,14 @@
.TH gmx-covar 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-covar 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-covar - Calculate and diagonalize the covariance matrix
+gmx-covar \- Calculate and diagonalize the covariance matrix
......@@ -393,7 +393,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-current.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-current.1
+++ gromacs-5.0.1/docs/man/man1/gmx-current.1
@@ -1,15 +1,15 @@
.TH gmx-current 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-current 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-current - Calculate dielectric constants and current autocorrelation function
+gmx-current \- Calculate dielectric constants and current autocorrelation function
......@@ -421,7 +421,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-densmap.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-densmap.1
+++ gromacs-5.0.1/docs/man/man1/gmx-densmap.1
@@ -1,15 +1,15 @@
.TH gmx-densmap 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-densmap 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-densmap - Calculate 2D planar or axial-radial density maps
+gmx-densmap \- Calculate 2D planar or axial-radial density maps
......@@ -449,7 +449,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-densorder.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-densorder.1
+++ gromacs-5.0.1/docs/man/man1/gmx-densorder.1
@@ -1,16 +1,16 @@
.TH gmx-densorder 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-densorder 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-densorder - Calculate surface fluctuations
+gmx-densorder \- Calculate surface fluctuations
......@@ -479,7 +479,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-dielectric.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-dielectric.1
+++ gromacs-5.0.1/docs/man/man1/gmx-dielectric.1
@@ -1,15 +1,15 @@
.TH gmx-dielectric 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-dielectric 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-dielectric - Calculate frequency dependent dielectric constants
+gmx-dielectric \- Calculate frequency dependent dielectric constants
......@@ -507,7 +507,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-dipoles.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-dipoles.1
+++ gromacs-5.0.1/docs/man/man1/gmx-dipoles.1
@@ -1,22 +1,22 @@
.TH gmx-dipoles 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-dipoles 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-dipoles - Compute the total dipole plus fluctuations
+gmx-dipoles \- Compute the total dipole plus fluctuations
......@@ -549,7 +549,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-disre.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-disre.1
+++ gromacs-5.0.1/docs/man/man1/gmx-disre.1
@@ -1,14 +1,14 @@
.TH gmx-disre 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-disre 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-disre - Analyze distance restraints
+gmx-disre \- Analyze distance restraints
......@@ -575,7 +575,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-distance.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-distance.1
+++ gromacs-5.0.1/docs/man/man1/gmx-distance.1
@@ -1,15 +1,15 @@
.TH gmx-distance 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-distance 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-distance - Calculate distances between pairs of positions
+gmx-distance \- Calculate distances between pairs of positions
......@@ -603,7 +603,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-do_dssp.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-do_dssp.1
+++ gromacs-5.0.1/docs/man/man1/gmx-do_dssp.1
@@ -1,14 +1,14 @@
.TH gmx-do_dssp 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-do_dssp 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-do_dssp - Assign secondary structure and calculate solvent accessible surface area
+gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area
......@@ -629,7 +629,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-dos.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-dos.1
+++ gromacs-5.0.1/docs/man/man1/gmx-dos.1
@@ -1,15 +1,15 @@
.TH gmx-dos 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-dos 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-dos - Analyze density of states and properties based on that
+gmx-dos \- Analyze density of states and properties based on that
......@@ -657,7 +657,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-dump.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-dump.1
+++ gromacs-5.0.1/docs/man/man1/gmx-dump.1
@@ -1,11 +1,11 @@
.TH gmx-dump 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-dump 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-dump - Make binary files human readable
+gmx-dump \- Make binary files human readable
......@@ -677,7 +677,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-dyecoupl.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-dyecoupl.1
+++ gromacs-5.0.1/docs/man/man1/gmx-dyecoupl.1
@@ -1,13 +1,13 @@
.TH gmx-dyecoupl 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-dyecoupl 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-dyecoupl - Extract dye dynamics from trajectories
+gmx-dyecoupl \- Extract dye dynamics from trajectories
......@@ -701,7 +701,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-dyndom.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-dyndom.1
+++ gromacs-5.0.1/docs/man/man1/gmx-dyndom.1
@@ -1,12 +1,12 @@
.TH gmx-dyndom 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-dyndom 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-dyndom - Interpolate and extrapolate structure rotations
+gmx-dyndom \- Interpolate and extrapolate structure rotations
......@@ -723,7 +723,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-editconf.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-editconf.1
+++ gromacs-5.0.1/docs/man/man1/gmx-editconf.1
@@ -1,18 +1,18 @@
.TH gmx-editconf 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-editconf 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-editconf - Convert and manipulates structure files
+gmx-editconf \- Convert and manipulates structure files
......@@ -757,7 +757,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-eneconv.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-eneconv.1
+++ gromacs-5.0.1/docs/man/man1/gmx-eneconv.1
@@ -1,12 +1,12 @@
.TH gmx-eneconv 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-eneconv 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-eneconv - Convert energy files
+gmx-eneconv \- Convert energy files
......@@ -779,7 +779,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-enemat.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-enemat.1
+++ gromacs-5.0.1/docs/man/man1/gmx-enemat.1
@@ -1,16 +1,16 @@
.TH gmx-enemat 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-enemat 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-enemat - Extract an energy matrix from an energy file
+gmx-enemat \- Extract an energy matrix from an energy file
......@@ -809,7 +809,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-energy.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-energy.1
+++ gromacs-5.0.1/docs/man/man1/gmx-energy.1
@@ -1,21 +1,21 @@
.TH gmx-energy 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-energy 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-energy - Writes energies to xvg files and display averages
+gmx-energy \- Writes energies to xvg files and display averages
......@@ -849,7 +849,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-filter.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-filter.1
+++ gromacs-5.0.1/docs/man/man1/gmx-filter.1
@@ -1,13 +1,13 @@
.TH gmx-filter 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-filter 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-filter - Frequency filter trajectories, useful for making smooth movies
+gmx-filter \- Frequency filter trajectories, useful for making smooth movies
......@@ -873,7 +873,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-freevolume.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-freevolume.1
+++ gromacs-5.0.1/docs/man/man1/gmx-freevolume.1
@@ -1,13 +1,13 @@
.TH gmx-freevolume 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-freevolume 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-freevolume - Calculate free volume
+gmx-freevolume \- Calculate free volume
......@@ -897,7 +897,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-gangle.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-gangle.1
+++ gromacs-5.0.1/docs/man/man1/gmx-gangle.1
@@ -1,14 +1,14 @@
.TH gmx-gangle 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-gangle 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-gangle - Calculate angles
+gmx-gangle \- Calculate angles
......@@ -923,7 +923,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-genconf.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-genconf.1
+++ gromacs-5.0.1/docs/man/man1/gmx-genconf.1
@@ -1,13 +1,13 @@
.TH gmx-genconf 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-genconf 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-genconf - Multiply a conformation in 'random' orientations
+gmx-genconf \- Multiply a conformation in 'random' orientations
......@@ -947,7 +947,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-genion.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-genion.1
+++ gromacs-5.0.1/docs/man/man1/gmx-genion.1
@@ -1,13 +1,13 @@
.TH gmx-genion 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-genion 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-genion - Generate monoatomic ions on energetically favorable positions
+gmx-genion \- Generate monoatomic ions on energetically favorable positions
......@@ -971,7 +971,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-genrestr.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-genrestr.1
+++ gromacs-5.0.1/docs/man/man1/gmx-genrestr.1
@@ -1,13 +1,13 @@
.TH gmx-genrestr 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-genrestr 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-genrestr - Generate position restraints or distance restraints for index groups
+gmx-genrestr \- Generate position restraints or distance restraints for index groups
......@@ -995,7 +995,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-grompp.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-grompp.1
+++ gromacs-5.0.1/docs/man/man1/gmx-grompp.1
@@ -1,15 +1,15 @@
.TH gmx-grompp 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-grompp 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-grompp - Make a run input file
+gmx-grompp \- Make a run input file
......@@ -1023,7 +1023,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-gyrate.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-gyrate.1
+++ gromacs-5.0.1/docs/man/man1/gmx-gyrate.1
@@ -1,14 +1,14 @@
.TH gmx-gyrate 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-gyrate 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-gyrate - Calculate the radius of gyration
+gmx-gyrate \- Calculate the radius of gyration
......@@ -1049,7 +1049,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-h2order.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-h2order.1
+++ gromacs-5.0.1/docs/man/man1/gmx-h2order.1
@@ -1,12 +1,12 @@
.TH gmx-h2order 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-h2order 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-h2order - Compute the orientation of water molecules
+gmx-h2order \- Compute the orientation of water molecules
......@@ -1071,7 +1071,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-hbond.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-hbond.1
+++ gromacs-5.0.1/docs/man/man1/gmx-hbond.1
@@ -1,21 +1,21 @@
.TH gmx-hbond 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-hbond 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-hbond - Compute and analyze hydrogen bonds
+gmx-hbond \- Compute and analyze hydrogen bonds
......@@ -1111,7 +1111,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-helix.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-helix.1
+++ gromacs-5.0.1/docs/man/man1/gmx-helix.1
@@ -1,13 +1,13 @@
.TH gmx-helix 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-helix 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-helix - Calculate basic properties of alpha helices
+gmx-helix \- Calculate basic properties of alpha helices
......@@ -1135,7 +1135,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-helixorient.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-helixorient.1
+++ gromacs-5.0.1/docs/man/man1/gmx-helixorient.1
@@ -1,14 +1,14 @@
.TH gmx-helixorient 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-helixorient 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-helixorient - Calculate local pitch/bending/rotation/orientation inside helices
+gmx-helixorient \- Calculate local pitch/bending/rotation/orientation inside helices
......@@ -1161,7 +1161,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-help.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-help.1
+++ gromacs-5.0.1/docs/man/man1/gmx-help.1
@@ -1,6 +1,6 @@
.TH gmx-help 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-help 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-help - Print help information
+gmx-help \- Print help information
......@@ -1173,7 +1173,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-hydorder.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-hydorder.1
+++ gromacs-5.0.1/docs/man/man1/gmx-hydorder.1
@@ -1,14 +1,14 @@
.TH gmx-hydorder 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-hydorder 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-hydorder - Compute tetrahedrality parameters around a given atom
+gmx-hydorder \- Compute tetrahedrality parameters around a given atom
......@@ -1199,7 +1199,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-insert-molecules.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-insert-molecules.1
+++ gromacs-5.0.1/docs/man/man1/gmx-insert-molecules.1
@@ -1,13 +1,13 @@
.TH gmx-insert-molecules 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-insert-molecules 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-insert-molecules - Insert molecules into existing vacancies
+gmx-insert-molecules \- Insert molecules into existing vacancies
......@@ -1223,7 +1223,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-lie.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-lie.1
+++ gromacs-5.0.1/docs/man/man1/gmx-lie.1
@@ -1,11 +1,11 @@
.TH gmx-lie 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-lie 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-lie - Estimate free energy from linear combinations
+gmx-lie \- Estimate free energy from linear combinations
......@@ -1243,7 +1243,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-make_edi.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-make_edi.1
+++ gromacs-5.0.1/docs/man/man1/gmx-make_edi.1
@@ -1,20 +1,20 @@
.TH gmx-make_edi 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-make_edi 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-make_edi - Generate input files for essential dynamics sampling
+gmx-make_edi \- Generate input files for essential dynamics sampling
......@@ -1281,7 +1281,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-make_ndx.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-make_ndx.1
+++ gromacs-5.0.1/docs/man/man1/gmx-make_ndx.1
@@ -1,10 +1,10 @@
.TH gmx-make_ndx 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-make_ndx 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-make_ndx - Make index files
+gmx-make_ndx \- Make index files
......@@ -1299,7 +1299,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-mdmat.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-mdmat.1
+++ gromacs-5.0.1/docs/man/man1/gmx-mdmat.1
@@ -1,12 +1,12 @@
.TH gmx-mdmat 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-mdmat 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-mdmat - Calculate residue contact maps
+gmx-mdmat \- Calculate residue contact maps
......@@ -1321,7 +1321,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-mdrun.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-mdrun.1
+++ gromacs-5.0.1/docs/man/man1/gmx-mdrun.1
@@ -1,30 +1,30 @@
.TH gmx-mdrun 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-mdrun 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-mdrun - Perform a simulation, do a normal mode analysis or an energy minimization
+gmx-mdrun \- Perform a simulation, do a normal mode analysis or an energy minimization
......@@ -1379,7 +1379,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-mindist.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-mindist.1
+++ gromacs-5.0.1/docs/man/man1/gmx-mindist.1
@@ -1,16 +1,16 @@
.TH gmx-mindist 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-mindist 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-mindist - Calculate the minimum distance between two groups
+gmx-mindist \- Calculate the minimum distance between two groups
......@@ -1409,7 +1409,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-mk_angndx.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-mk_angndx.1
+++ gromacs-5.0.1/docs/man/man1/gmx-mk_angndx.1
@@ -1,10 +1,10 @@
.TH gmx-mk_angndx 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-mk_angndx 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-mk_angndx - Generate index files for 'gmx angle'
+gmx-mk_angndx \- Generate index files for 'gmx angle'
......@@ -1427,7 +1427,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-morph.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-morph.1
+++ gromacs-5.0.1/docs/man/man1/gmx-morph.1
@@ -1,12 +1,12 @@
.TH gmx-morph 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-morph 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-morph - Interpolate linearly between conformations
+gmx-morph \- Interpolate linearly between conformations
......@@ -1449,7 +1449,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-msd.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-msd.1
+++ gromacs-5.0.1/docs/man/man1/gmx-msd.1
@@ -1,14 +1,14 @@
.TH gmx-msd 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-msd 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-msd - Calculates mean square displacements
+gmx-msd \- Calculates mean square displacements
......@@ -1475,7 +1475,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-nmeig.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-nmeig.1
+++ gromacs-5.0.1/docs/man/man1/gmx-nmeig.1
@@ -1,13 +1,13 @@
.TH gmx-nmeig 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-nmeig 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-nmeig - Diagonalize the Hessian for normal mode analysis
+gmx-nmeig \- Diagonalize the Hessian for normal mode analysis
......@@ -1499,7 +1499,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-nmens.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-nmens.1
+++ gromacs-5.0.1/docs/man/man1/gmx-nmens.1
@@ -1,12 +1,12 @@
.TH gmx-nmens 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-nmens 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-nmens - Generate an ensemble of structures from the normal modes
+gmx-nmens \- Generate an ensemble of structures from the normal modes
......@@ -1521,7 +1521,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-nmtraj.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-nmtraj.1
+++ gromacs-5.0.1/docs/man/man1/gmx-nmtraj.1
@@ -1,12 +1,12 @@
.TH gmx-nmtraj 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-nmtraj 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-nmtraj - Generate a virtual oscillating trajectory from an eigenvector
+gmx-nmtraj \- Generate a virtual oscillating trajectory from an eigenvector
......@@ -1543,7 +1543,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-order.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-order.1
+++ gromacs-5.0.1/docs/man/man1/gmx-order.1
@@ -1,15 +1,15 @@
.TH gmx-order 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-order 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-order - Compute the order parameter per atom for carbon tails
+gmx-order \- Compute the order parameter per atom for carbon tails
......@@ -1571,7 +1571,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-pdb2gmx.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-pdb2gmx.1
+++ gromacs-5.0.1/docs/man/man1/gmx-pdb2gmx.1
@@ -1,18 +1,18 @@
.TH gmx-pdb2gmx 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-pdb2gmx 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-pdb2gmx - Convert coordinate files to topology and FF-compliant coordinate files
+gmx-pdb2gmx \- Convert coordinate files to topology and FF-compliant coordinate files
......@@ -1605,7 +1605,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-pme_error.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-pme_error.1
+++ gromacs-5.0.1/docs/man/man1/gmx-pme_error.1
@@ -1,11 +1,11 @@
.TH gmx-pme_error 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-pme_error 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-pme_error - Estimate the error of using PME with a given input file
+gmx-pme_error \- Estimate the error of using PME with a given input file
......@@ -1625,7 +1625,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-polystat.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-polystat.1
+++ gromacs-5.0.1/docs/man/man1/gmx-polystat.1
@@ -1,13 +1,13 @@
.TH gmx-polystat 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-polystat 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-polystat - Calculate static properties of polymers
+gmx-polystat \- Calculate static properties of polymers
......@@ -1649,7 +1649,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-potential.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-potential.1
+++ gromacs-5.0.1/docs/man/man1/gmx-potential.1
@@ -1,14 +1,14 @@
.TH gmx-potential 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-potential 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-potential - Calculate the electrostatic potential across the box
+gmx-potential \- Calculate the electrostatic potential across the box
......@@ -1675,7 +1675,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-protonate.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-protonate.1
+++ gromacs-5.0.1/docs/man/man1/gmx-protonate.1
@@ -1,11 +1,11 @@
.TH gmx-protonate 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-protonate 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-protonate - Protonate structures
+gmx-protonate \- Protonate structures
......@@ -1695,7 +1695,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-rama.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-rama.1
+++ gromacs-5.0.1/docs/man/man1/gmx-rama.1
@@ -1,11 +1,11 @@
.TH gmx-rama 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-rama 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-rama - Compute Ramachandran plots
+gmx-rama \- Compute Ramachandran plots
......@@ -1715,7 +1715,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-rdf.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-rdf.1
+++ gromacs-5.0.1/docs/man/man1/gmx-rdf.1
@@ -1,14 +1,14 @@
.TH gmx-rdf 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-rdf 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-rdf - Calculate radial distribution functions
+gmx-rdf \- Calculate radial distribution functions
......@@ -1741,7 +1741,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-rms.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-rms.1
+++ gromacs-5.0.1/docs/man/man1/gmx-rms.1
@@ -1,17 +1,17 @@
.TH gmx-rms 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-rms 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-rms - Calculate RMSDs with a reference structure and RMSD matrices
+gmx-rms \- Calculate RMSDs with a reference structure and RMSD matrices
......@@ -1773,7 +1773,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-rmsdist.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-rmsdist.1
+++ gromacs-5.0.1/docs/man/man1/gmx-rmsdist.1
@@ -1,15 +1,15 @@
.TH gmx-rmsdist 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-rmsdist 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-rmsdist - Calculate atom pair distances averaged with power -2, -3 or -6
+gmx-rmsdist \- Calculate atom pair distances averaged with power \-2, \-3 or \-6
......@@ -1801,7 +1801,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-rmsf.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-rmsf.1
+++ gromacs-5.0.1/docs/man/man1/gmx-rmsf.1
@@ -1,13 +1,13 @@
.TH gmx-rmsf 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-rmsf 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-rmsf - Calculate atomic fluctuations
+gmx-rmsf \- Calculate atomic fluctuations
......@@ -1825,7 +1825,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-rotacf.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-rotacf.1
+++ gromacs-5.0.1/docs/man/man1/gmx-rotacf.1
@@ -1,13 +1,13 @@
.TH gmx-rotacf 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-rotacf 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-rotacf - Calculate the rotational correlation function for molecules
+gmx-rotacf \- Calculate the rotational correlation function for molecules
......@@ -1849,7 +1849,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-rotmat.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-rotmat.1
+++ gromacs-5.0.1/docs/man/man1/gmx-rotmat.1
@@ -1,12 +1,12 @@
.TH gmx-rotmat 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-rotmat 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-rotmat - Plot the rotation matrix for fitting to a reference structure
+gmx-rotmat \- Plot the rotation matrix for fitting to a reference structure
......@@ -1871,7 +1871,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-saltbr.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-saltbr.1
+++ gromacs-5.0.1/docs/man/man1/gmx-saltbr.1
@@ -1,11 +1,11 @@
.TH gmx-saltbr 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-saltbr 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-saltbr - Compute salt bridges
+gmx-saltbr \- Compute salt bridges
......@@ -1891,7 +1891,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-sans.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-sans.1
+++ gromacs-5.0.1/docs/man/man1/gmx-sans.1
@@ -1,15 +1,15 @@
.TH gmx-sans 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-sans 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-sans - Compute small angle neutron scattering spectra
+gmx-sans \- Compute small angle neutron scattering spectra
......@@ -1919,7 +1919,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-sasa.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-sasa.1
+++ gromacs-5.0.1/docs/man/man1/gmx-sasa.1
@@ -1,15 +1,15 @@
.TH gmx-sasa 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-sasa 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-sasa - Compute solvent accessible surface area
+gmx-sasa \- Compute solvent accessible surface area
......@@ -1947,7 +1947,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-saxs.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-saxs.1
+++ gromacs-5.0.1/docs/man/man1/gmx-saxs.1
@@ -1,12 +1,12 @@
.TH gmx-saxs 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-saxs 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-saxs - Compute small angle X-ray scattering spectra
+gmx-saxs \- Compute small angle X-ray scattering spectra
......@@ -1969,7 +1969,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-select.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-select.1
+++ gromacs-5.0.1/docs/man/man1/gmx-select.1
@@ -1,16 +1,16 @@
.TH gmx-select 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-select 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-select - Print general information about selections
+gmx-select \- Print general information about selections
......@@ -1999,7 +1999,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-sigeps.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-sigeps.1
+++ gromacs-5.0.1/docs/man/man1/gmx-sigeps.1
@@ -1,12 +1,12 @@
.TH gmx-sigeps 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-sigeps 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-sigeps - Convert c6/12 or c6/cn combinations to and from sigma/epsilon
+gmx-sigeps \- Convert c6/12 or c6/cn combinations to and from sigma/epsilon
......@@ -2021,7 +2021,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-solvate.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-solvate.1
+++ gromacs-5.0.1/docs/man/man1/gmx-solvate.1
@@ -1,12 +1,12 @@
.TH gmx-solvate 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-solvate 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-solvate - Solvate a system
+gmx-solvate \- Solvate a system
......@@ -2043,7 +2043,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-sorient.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-sorient.1
+++ gromacs-5.0.1/docs/man/man1/gmx-sorient.1
@@ -1,14 +1,14 @@
.TH gmx-sorient 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-sorient 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-sorient - Analyze solvent orientation around solutes
+gmx-sorient \- Analyze solvent orientation around solutes
......@@ -2069,7 +2069,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-spatial.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-spatial.1
+++ gromacs-5.0.1/docs/man/man1/gmx-spatial.1
@@ -1,12 +1,12 @@
.TH gmx-spatial 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-spatial 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-spatial - Calculate the spatial distribution function
+gmx-spatial \- Calculate the spatial distribution function
......@@ -2091,7 +2091,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-spol.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-spol.1
+++ gromacs-5.0.1/docs/man/man1/gmx-spol.1
@@ -1,13 +1,13 @@
.TH gmx-spol 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-spol 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-spol - Analyze solvent dipole orientation and polarization around solutes
+gmx-spol \- Analyze solvent dipole orientation and polarization around solutes
......@@ -2115,7 +2115,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-tcaf.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-tcaf.1
+++ gromacs-5.0.1/docs/man/man1/gmx-tcaf.1
@@ -1,15 +1,15 @@
.TH gmx-tcaf 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-tcaf 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-tcaf - Calculate viscosities of liquids
+gmx-tcaf \- Calculate viscosities of liquids
......@@ -2143,7 +2143,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-traj.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-traj.1
+++ gromacs-5.0.1/docs/man/man1/gmx-traj.1
@@ -1,17 +1,17 @@
.TH gmx-traj 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-traj 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-traj - Plot x, v, f, box, temperature and rotational energy from trajectories
+gmx-traj \- Plot x, v, f, box, temperature and rotational energy from trajectories
......@@ -2175,7 +2175,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-trjcat.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-trjcat.1
+++ gromacs-5.0.1/docs/man/man1/gmx-trjcat.1
@@ -1,13 +1,13 @@
.TH gmx-trjcat 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-trjcat 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-trjcat - Concatenate trajectory files
+gmx-trjcat \- Concatenate trajectory files
......@@ -2199,7 +2199,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-trjconv.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-trjconv.1
+++ gromacs-5.0.1/docs/man/man1/gmx-trjconv.1
@@ -1,20 +1,20 @@
.TH gmx-trjconv 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-trjconv 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-trjconv - Convert and manipulates trajectory files
+gmx-trjconv \- Convert and manipulates trajectory files
......@@ -2237,7 +2237,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-trjorder.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-trjorder.1
+++ gromacs-5.0.1/docs/man/man1/gmx-trjorder.1
@@ -1,13 +1,13 @@
.TH gmx-trjorder 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-trjorder 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-trjorder - Order molecules according to their distance to a group
+gmx-trjorder \- Order molecules according to their distance to a group
......@@ -2261,7 +2261,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-tune_pme.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-tune_pme.1
+++ gromacs-5.0.1/docs/man/man1/gmx-tune_pme.1
@@ -1,34 +1,34 @@
.TH gmx-tune_pme 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-tune_pme 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-tune_pme - Time mdrun as a function of PME ranks to optimize settings
+gmx-tune_pme \- Time mdrun as a function of PME ranks to optimize settings
......@@ -2292,7 +2292,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-tune_pme.1
- [-rmax <real>] [-rmin <real>] [-[no]scalevdw]
- [-ntpr <int>] [-steps <int>] [-resetstep <int>]
- [-simsteps <int>] [-[no]launch] [-[no]bench]
- [-[no]append] [-[no]cpnum]
- [-[no]check] [-[no]append] [-[no]cpnum]
+gmx tune_pme [\-p [<.out>]] [\-err [<.log>]] [\-so [<.tpr/.tpb/...>]]
+ [\-s [<.tpr/.tpb/...>]] [\-o [<.trr/.cpt/...>]]
+ [\-x [<.xtc/.tng>]] [\-cpi [<.cpt>]] [\-cpo [<.cpt>]]
......@@ -2318,7 +2318,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-tune_pme.1
+ [\-rmax <real>] [\-rmin <real>] [\-[no]scalevdw]
+ [\-ntpr <int>] [\-steps <int>] [\-resetstep <int>]
+ [\-simsteps <int>] [\-[no]launch] [\-[no]bench]
+ [\-[no]append] [\-[no]cpnum]
+ [\-[no]check] [\-[no]append] [\-[no]cpnum]
.SH DESCRIPTION
For a given number \fB\-np\fR or \fB\-ntmpi\fR of ranks, \fBgmx tune_pme\fR systematically times \fBgmx mdrun\fR with various numbers of PME\-only ranks and determines which setting is fastest. It will also test whether performance can be enhanced by shifting load from the reciprocal to the real space part of the Ewald sum. Simply pass your \fB.tpr\fR file to \fBgmx tune_pme\fR together with other options for \fBgmx mdrun\fR as needed.
......@@ -2327,7 +2327,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-vanhove.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-vanhove.1
+++ gromacs-5.0.1/docs/man/man1/gmx-vanhove.1
@@ -1,15 +1,15 @@
.TH gmx-vanhove 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-vanhove 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-vanhove - Compute Van Hove displacement and correlation functions
+gmx-vanhove \- Compute Van Hove displacement and correlation functions
......@@ -2355,7 +2355,7 @@ Index: gromacs-5.0.1/docs/man/man1/gmx-velacc.1
--- gromacs-5.0.1.orig/docs/man/man1/gmx-velacc.1
+++ gromacs-5.0.1/docs/man/man1/gmx-velacc.1
@@ -1,14 +1,14 @@
.TH gmx-velacc 1 "" "VERSION 5.0.1" "GROMACS Manual"
.TH gmx-velacc 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
-gmx-velacc - Calculate velocity autocorrelation functions