[gromacs/el5/master] Update to 4.5.2.
Jussi Lehtola
jussilehtola at fedoraproject.org
Mon Nov 1 14:46:09 UTC 2010
commit 32fb4a677a8ce8e59ca15da97fcc3952eec28439
Author: Jussi Lehtola <jussilehtola at fedoraproject.org>
Date: Mon Nov 1 16:46:01 2010 +0200
Update to 4.5.2.
gromacs-configure.patch | 17 ---
gromacs-gmxdemo.patch | 301 +++++++++++++++++++++++++++++++++++++++-------
gromacs.spec | 5 +-
3 files changed, 259 insertions(+), 64 deletions(-)
---
diff --git a/gromacs-gmxdemo.patch b/gromacs-gmxdemo.patch
index 7160fb2..f146ab7 100644
--- a/gromacs-gmxdemo.patch
+++ b/gromacs-gmxdemo.patch
@@ -1,106 +1,315 @@
-diff -up gromacs-4.0.3/share/tutor/gmxdemo/demo.orig gromacs-4.0.3/share/tutor/gmxdemo/demo
---- gromacs-4.0.3/share/tutor/gmxdemo/demo.orig 2006-02-15 23:48:34.000000000 +0200
-+++ gromacs-4.0.3/share/tutor/gmxdemo/demo 2009-01-19 16:52:35.000000000 +0200
-@@ -80,9 +80,9 @@ set ans = $<
+diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tutor/gmxdemo/demo
+--- gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo 2010-09-29 14:35:03.000000000 +0300
++++ gromacs-4.5.2/share/tutor/gmxdemo/demo 2010-11-01 14:04:34.833273502 +0200
+@@ -58,10 +58,10 @@ cat << _EOF_
+ -----------------------------------------------------------------
+ Before we can start any simulation we need a molecular toplogy
+ file. This topology file ( .top extension ) is generated by the
+-program pdb2gmx. The only input file of the pdb2gmx program is the pdb
++program g_pdb2gmx. The only input file of the g_pdb2gmx program is the pdb
+ file of our peptide ( .pdb extension ).
- echo "Starting pdb2gmx"
+-Because most pdb files do not contain all hydrogen atoms, the pdb2gmx
++Because most pdb files do not contain all hydrogen atoms, the g_pdb2gmx
+ program will also add them to our peptide. The output file which
+ contains the structure of the peptide when hydrogen atoms are added is a
+ gromos structure file ( .gro extension )
+@@ -72,22 +72,22 @@ _EOF_
+
+ if ( $?DISPLAY ) then
+ echo "You seem to have the DISPLAY variable is set, so we will"
+- echo "pop up a window with the output of the pdb2gmx program"
++ echo "pop up a window with the output of the g_pdb2gmx program"
+ endif
+ echo -n "Press <enter>"
+ set ans = $<
+
+
+-echo "Starting pdb2gmx"
++echo "Starting g_pdb2gmx"
if ( $?DISPLAY ) then
- xterm -title pdb2gmx -sb -e tail +0f output.pdb2gmx &
-+ xterm -title g_pdb2gmx -sb -e tail +0f output.pdb2gmx &
++ xterm -title g_pdb2gmx -sb -e tail +0f output.g_pdb2gmx &
+ endif
+-pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.pdb2gmx << KOKO
++g_pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.g_pdb2gmx << KOKO
+ 1
+ 1
+ KOKO
+
+-echo "pdb2gmx finished"
++echo "g_pdb2gmx finished"
+ echo -n "Press <enter>"
+ set ans = $<
+
+@@ -99,14 +99,14 @@ cat << _EOF_
+ -----------------------------------------------------------------
+ -----------------------------------------------------------------
+ Because a simulation of a peptide in vacua is a bit unrealistic, we
+-have to solvate our peptide in a box of water. genbox is the program
++have to solvate our peptide in a box of water. g_genbox is the program
+ we use to do this.
+
+-The genbox program reads the peptide structure file and an input file
+-containing the sizes of the desired water box. The output of genbox is
++The g_genbox program reads the peptide structure file and an input file
++containing the sizes of the desired water box. The output of g_genbox is
+ a gromos structure file of a peptide solvated in a box of water. The
+-genbox program also changes the topology file ( .top extension ) to
+-include water. First we will use the program editconf to define the
++g_genbox program also changes the topology file ( .top extension ) to
++include water. First we will use the program g_editconf to define the
+ right boxsize for our system.
+
+ -----------------------------------------------------------------
+@@ -114,22 +114,22 @@ right boxsize for our system.
+ _EOF_
+
+ if ( $?DISPLAY ) then
+- echo "The output of the genbox program should appear"
++ echo "The output of the g_genbox program should appear"
+ echo "in a separate xterm window"
endif
--echo 0 | pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.pdb2gmx
-+echo 0 | g_pdb2gmx -f ${MOL}.pdb -o ${MOL}.gro -p ${MOL}.top >& ! output.pdb2gmx
- echo "pdb2gmx finished"
+
echo -n "Press <enter>"
set ans = $<
-@@ -119,11 +119,11 @@ set ans = $<
- echo "Starting editconf and genbox..."
+-echo "Starting editconf and genbox..."
++echo "Starting g_editconf and g_genbox..."
if ( $?DISPLAY ) then
- xterm -title genbox -sb -e tail +0f output.genbox &
-+ xterm -title g_genbox -sb -e tail +0f output.genbox &
++ xterm -title g_genbox -sb -e tail +0f output.g_genbox &
endif
-editconf -f ${MOL}.gro -o ${MOL}.gro -d 0.5 >& ! output.genbox
-+g_editconf -f ${MOL}.gro -o ${MOL}.gro -d 0.5 >& ! output.genbox
++g_editconf -f ${MOL}.gro -o ${MOL}.gro -d 0.5 >& ! output.g_genbox
-genbox -cp ${MOL}.gro -cs -o ${MOL}_b4em.gro -p ${MOL}.top >>& ! output.genbox
-+g_genbox -cp ${MOL}.gro -cs -o ${MOL}_b4em.gro -p ${MOL}.top >>& ! output.genbox
++g_genbox -cp ${MOL}.gro -cs -o ${MOL}_b4em.gro -p ${MOL}.top >>& ! output.g_genbox
- echo "editconf and genbox finished"
+-echo "editconf and genbox finished"
++echo "g_editconf and g_genbox finished"
echo -n "Press <enter>"
-@@ -189,9 +189,9 @@ _EOF_
+ set ans = $<
- echo "Starting grompp..."
+@@ -142,7 +142,7 @@ cat << _EOF_
+ -----------------------------------------------------------------
+ In principle we can start a Molecular Dynamics simulation now. However
+ it is not very wise to do so, because our system is full of close
+-contacts. These close contacts are mainly a result of the genbox
++contacts. These close contacts are mainly a result of the g_genbox
+ program. The added solvent might have some close contacts with the
+ peptide resulting in very high repulsive energies. If we would start a
+ Molecular Dynamics (MD) simulation without energy minimisation the
+@@ -153,7 +153,7 @@ Energy Minimisation (EM). Energy minimis
+ coordinates of our system to remove high energies from our system.
+
+ Before we can start the Energy Minimisation we have to preprocess all
+-the input files with the GROMACS preprocessor named grompp. grompp
++the input files with the GROMACS preprocessor named g_g_grompp. g_g_grompp
+ preprocesses the topology file (.top), the structure file (.gro) and a
+ parameter file (.mdp) resulting in a binary topology file (.tpr
+ extension). This binary topology file contains all information for a
+@@ -163,7 +163,7 @@ simulation (in this case an energy minim
+ _EOF_
+
+ if ( $?DISPLAY ) then
+- echo "The output of the grompp program should appear"
++ echo "The output of the g_g_grompp program should appear"
+ echo "in a separate xterm window"
+ endif
+
+@@ -191,13 +191,13 @@ emtol = 1000.0
+ emstep = 0.01
+ _EOF_
+
+-echo "Starting grompp..."
++echo "Starting g_grompp..."
if ( $?DISPLAY ) then
- xterm -title grompp -sb -e tail +0f output.grompp_em &
-+ xterm -title g_grompp -sb -e tail +0f output.grompp_em &
++ xterm -title g_grompp -sb -e tail +0f output.g_grompp_em &
endif
-grompp -f em -c ${MOL}_b4em -p ${MOL} -o ${MOL}_em >& ! output.grompp_em
-+g_grompp -f em -c ${MOL}_b4em -p ${MOL} -o ${MOL}_em >& ! output.grompp_em
++g_grompp -f em -c ${MOL}_b4em -p ${MOL} -o ${MOL}_em >& ! output.g_grompp_em
- echo "grompp finished"
+-echo "grompp finished"
++echo "g_grompp finished"
echo -n "Press <enter>"
-@@ -230,9 +230,9 @@ set ans = $<
- echo "starting energy minimisation mdrun..."
+ set ans = $<
+
+@@ -210,8 +210,8 @@ cat << _EOF_
+ -----------------------------------------------------------------
+ Now the binary topology file is generated, we can start the energy
+ minimisation (EM). The program which performs the EM is called
+-mdrun. In fact all simulations are performed by the same program:
+-mdrun.
++g_mdrun. In fact all simulations are performed by the same program:
++g_mdrun.
+
+ As the Energy Minimisation is running, watch the output of the
+ program. The first number ( from left to right ) is the number of the
+@@ -224,21 +224,21 @@ rapidly drops down, and converges, to a
+ _EOF_
+
+ if ( $?DISPLAY ) then
+- echo "The output of the mdrun program should appear"
++ echo "The output of the g_mdrun program should appear"
+ echo "in a separate xterm window"
+ endif
+
+ echo -n "Press <enter>"
+ set ans = $<
+
+-echo "starting energy minimisation mdrun..."
++echo "starting energy minimisation g_mdrun..."
if ( $?DISPLAY ) then
- xterm -title mdrun -sb -e tail +0f output.mdrun_em &
-+ xterm -title g_mdrun -sb -e tail +0f output.mdrun_em &
++ xterm -title g_mdrun -sb -e tail +0f output.g_mdrun_em &
endif
-mdrun -nice 4 -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4pr -v >& ! output.mdrun_em
-+g_mdrun -nice 4 -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4pr -v >& ! output.mdrun_em
++g_mdrun -nice 4 -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4pr -v >& ! output.g_mdrun_em
- echo "mdrun finished"
+-echo "mdrun finished"
++echo "g_mdrun finished"
echo -n "Press <enter>"
-@@ -316,9 +316,9 @@ _EOF_
+ set ans = $<
- echo "Starting grompp..."
+@@ -255,7 +255,7 @@ fixed. This is called position restraine
+
+ Position Restrained MD keeps the peptide fixed and lets all water
+ molecules equilibrate around the peptide in order to fill holes
+-etc. which were not filled by the genbox program.
++etc. which were not filled by the g_genbox program.
+
+ We are first going to preprocess the input files to generate the
+ binary topology. The input files are the topology file, the structure
+@@ -274,7 +274,7 @@ performed ( like EM, PR-MD and MD etc. )
+ _EOF_
+
+ if ( $?DISPLAY ) then
+- echo "The output of the grompp program should appear"
++ echo "The output of the g_g_grompp program should appear"
+ echo "in a separate xterm window"
+ endif
+
+@@ -318,12 +318,12 @@ gen_seed = 173529
+ _EOF_
+
+
+-echo "Starting grompp..."
++echo "Starting g_grompp..."
if ( $?DISPLAY ) then
- xterm -title grompp -sb -e tail +0f output.grompp_pr &
-+ xterm -title g_grompp -sb -e tail +0f output.grompp_pr &
++ xterm -title g_grompp -sb -e tail +0f output.g_grompp_pr &
endif
-grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.grompp_pr
-+g_grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.grompp_pr
- echo "grompp finished"
+-echo "grompp finished"
++g_grompp -f pr -c ${MOL}_b4pr -r ${MOL}_b4pr -p ${MOL} -o ${MOL}_pr >& ! output.g_grompp_pr
++echo "g_grompp finished"
+
+ echo -n "Press <enter>"
+ set ans = $<
+@@ -346,19 +346,19 @@ _EOF_
+
+ if ( $?DISPLAY ) then
+ echo "Because your DISPLAY variable is set, I will pop up a"
+- echo "window with the output of the mdrun program"
++ echo "window with the output of the g_mdrun program"
+ endif
echo -n "Press <enter>"
-@@ -350,9 +350,9 @@ set ans = $<
+ set ans = $<
- echo "starting mdrun..."
+-echo "starting mdrun..."
++echo "starting g_mdrun..."
if ( $?DISPLAY ) then
- xterm -title mdrun -sb -e tail +0f output.mdrun_pr &
-+ xterm -title g_mdrun -sb -e tail +0f output.mdrun_pr &
++ xterm -title g_mdrun -sb -e tail +0f output.g_mdrun_pr &
endif
-mdrun -nice 4 -s ${MOL}_pr -o ${MOL}_pr -c ${MOL}_b4md -v >& ! output.mdrun_pr
-+g_mdrun -nice 4 -s ${MOL}_pr -o ${MOL}_pr -c ${MOL}_b4md -v >& ! output.mdrun_pr
++g_mdrun -nice 4 -s ${MOL}_pr -o ${MOL}_pr -c ${MOL}_b4md -v >& ! output.g_mdrun_pr
- echo "mdrun finished"
+-echo "mdrun finished"
++echo "g_mdrun finished"
echo -n "Press <enter>"
-@@ -417,9 +417,9 @@ _EOF_
+ set ans = $<
+
+@@ -371,7 +371,7 @@ cat << _EOF_
+ -----------------------------------------------------------------
+ Now our complete system is finally ready for the actual Molecular
+ Dynamics simulation. We start again by preprocessing the input files
+-by the grompp program to generate the binary topology file (.tpb/.tpr
++by the g_g_grompp program to generate the binary topology file (.tpb/.tpr
+ extension).
+
+ -----------------------------------------------------------------
+@@ -379,7 +379,7 @@ extension).
+ _EOF_
- echo "Starting grompp..."
+ if ( $?DISPLAY ) then
+- echo "The output of the grompp program should appear"
++ echo "The output of the g_g_grompp program should appear"
+ echo "in a separate xterm window"
+ endif
+
+@@ -419,13 +419,13 @@ gen_temp = 300.0
+ gen_seed = 173529
+ _EOF_
+
+-echo "Starting grompp..."
++echo "Starting g_grompp..."
if ( $?DISPLAY ) then
- xterm -title grompp -sb -e tail +0f output.grompp_md &
-+ xterm -title g_grompp -sb -e tail +0f output.grompp_md &
++ xterm -title g_grompp -sb -e tail +0f output.g_grompp_md &
endif
-grompp -f md -c ${MOL}_b4md -p ${MOL} -o ${MOL}_md >& ! output.grompp_md
-+g_grompp -f md -c ${MOL}_b4md -p ${MOL} -o ${MOL}_md >& ! output.grompp_md
++g_grompp -f md -c ${MOL}_b4md -p ${MOL} -o ${MOL}_md >& ! output.g_grompp_md
- echo "grompp finished"
+-echo "grompp finished"
++echo "g_grompp finished"
echo -n "Press <enter>"
-@@ -449,9 +449,9 @@ set ans = $<
+ set ans = $<
+
+@@ -444,20 +444,20 @@ increasing ( the total number of steps i
+ _EOF_
+
+ if ( $?DISPLAY ) then
+- echo "The output of the mdrun program should appear"
++ echo "The output of the g_mdrun program should appear"
+ echo "in a separate xterm window"
+ endif
- echo "starting mdrun..."
+ echo -n "Press <enter>"
+ set ans = $<
+
+-echo "starting mdrun..."
++echo "starting g_mdrun..."
if ( $?DISPLAY ) then
- xterm -title mdrun -sb -e tail +0f output.mdrun_md &
-+ xterm -title g_mdrun -sb -e tail +0f output.mdrun_md &
++ xterm -title g_mdrun -sb -e tail +0f output.g_mdrun_md &
endif
-mdrun -nice 4 -s ${MOL}_md -o ${MOL}_md -c ${MOL}_after_md -v >& ! output.mdrun_md
-+g_mdrun -nice 4 -s ${MOL}_md -o ${MOL}_md -c ${MOL}_after_md -v >& ! output.mdrun_md
++g_mdrun -nice 4 -s ${MOL}_md -o ${MOL}_md -c ${MOL}_after_md -v >& ! output.g_mdrun_md
- echo "mdrun finished"
+-echo "mdrun finished"
++echo "g_mdrun finished"
echo -n "Press <enter>"
-@@ -493,7 +493,7 @@ _EOF_
+ set ans = $<
+
+@@ -472,10 +472,10 @@ We are finished simulating, and we are g
+ trajectory. The trajectory file ( .trj extension ) contains all
+ coordinates, velocities and forces of all the atoms in our system.
+
+-The next program we are going run is ngmx. ngmx is a very simple
++The next program we are going run is g_ngmx. g_ngmx is a very simple
+ trajectory viewer.
+
+-Once the ngmx program has been started you need to click on a few
++Once the g_ngmx program has been started you need to click on a few
+ buttons to view your trajectory.
+
+ 1. Once the program has been started a dialog box shows up. Click on
+@@ -497,7 +497,7 @@ _EOF_
if ( $?DISPLAY ) then
echo Starting Trajectory viewer...
diff --git a/gromacs.spec b/gromacs.spec
index 6ff44e8..5e795b0 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -1,5 +1,5 @@
Name: gromacs
-Version: 4.5.1
+Version: 4.5.2
Release: 1%{?dist}
Summary: Fast, Free and Flexible Molecular Dynamics
Group: Applications/Engineering
@@ -428,6 +428,9 @@ rm -rf %{buildroot}
%changelog
+* Mon Nov 01 2010 Jussi Lehtola <jussilehtola at fedoraproject.org> - 4.5.2-1
+- Update to 4.5.2.
+
* Sat Oct 09 2010 Jussi Lehtola <jussilehtola at fedoraproject.org> - 4.5.1-1
- Update to 4.5.1.
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