From e1479ef9e5e9e25963c64871f8334a465da15de8 Mon Sep 17 00:00:00 2001 From: Jussi Lehtola Date: Mar 23 2011 14:54:52 +0000 Subject: Update to 4.5.4. --- diff --git a/.gitignore b/.gitignore index eb9c53a..1bf2a8a 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,5 @@ manual-4.0.pdf /gromacs-4.5.1.tar.gz /gromacs-4.5.2.tar.gz /gromacs-4.5.3.tar.gz +/gromacs-4.5.4.tar.gz +/manual-4.5.4.pdf diff --git a/gromacs-GMXRC.patch b/gromacs-GMXRC.patch index a185174..97b3b05 100644 --- a/gromacs-GMXRC.patch +++ b/gromacs-GMXRC.patch @@ -1,26 +1,30 @@ ---- gromacs-4.0_rc2/scripts/GMXRC.csh.in.orig 2001-08-18 14:07:31.000000000 +0300 -+++ gromacs-4.0_rc2/scripts/GMXRC.csh.in 2008-09-28 15:33:26.000000000 +0300 +diff -up gromacs-4.5.4/scripts/GMXRC.bash.in.orig gromacs-4.5.4/scripts/GMXRC.bash.in +--- gromacs-4.5.4/scripts/GMXRC.bash.in.orig 2011-03-15 14:44:30.000000000 +0200 ++++ gromacs-4.5.4/scripts/GMXRC.bash.in 2011-03-23 15:23:47.460843630 +0200 +@@ -1,3 +1,4 @@ ++#!/bin/bash + # bash configuration file for Gromacs + # First we remove old gromacs stuff from the paths + # by selecting everything else. +diff -up gromacs-4.5.4/scripts/GMXRC.csh.in.orig gromacs-4.5.4/scripts/GMXRC.csh.in +--- gromacs-4.5.4/scripts/GMXRC.csh.in.orig 2011-03-15 14:44:30.000000000 +0200 ++++ gromacs-4.5.4/scripts/GMXRC.csh.in 2011-03-23 15:23:24.515816712 +0200 @@ -1,3 +1,4 @@ +#!/bin/csh # csh/tcsh configuration file for Gromacs. # First we remove previous Gromacs stuff from paths # by selecting everything else. ---- gromacs-4.0_rc2/scripts/GMXRC.bash.in.orig 2001-08-18 14:07:31.000000000 +0300 -+++ gromacs-4.0_rc2/scripts/GMXRC.bash.in 2008-09-28 15:33:08.000000000 +0300 -@@ -1,3 +1,4 @@ -+#!/bin/bash - # zsh configuration file for Gromacs - # First we remove old gromacs stuff from the paths - # by selecting everything else. ---- gromacs-4.0_rc2/scripts/GMXRC.in.orig 2001-08-18 14:07:31.000000000 +0300 -+++ gromacs-4.0_rc2/scripts/GMXRC.in 2008-09-28 15:33:44.000000000 +0300 +diff -up gromacs-4.5.4/scripts/GMXRC.in.orig gromacs-4.5.4/scripts/GMXRC.in +--- gromacs-4.5.4/scripts/GMXRC.in.orig 2011-03-15 14:44:30.000000000 +0200 ++++ gromacs-4.5.4/scripts/GMXRC.in 2011-03-23 15:23:58.499338216 +0200 @@ -1,3 +1,4 @@ +#!/bin/sh # This is a convenience script to determine which # type of shell you have, and then run GMXRC.[csh|bash|zsh] # from the Gromacs binary directory. ---- gromacs-4.0_rc2/scripts/GMXRC.zsh.in.orig 2001-08-18 14:07:31.000000000 +0300 -+++ gromacs-4.0_rc2/scripts/GMXRC.zsh.in 2008-09-28 15:33:34.000000000 +0300 +diff -up gromacs-4.5.4/scripts/GMXRC.zsh.in.orig gromacs-4.5.4/scripts/GMXRC.zsh.in +--- gromacs-4.5.4/scripts/GMXRC.zsh.in.orig 2011-03-15 14:44:30.000000000 +0200 ++++ gromacs-4.5.4/scripts/GMXRC.zsh.in 2011-03-23 15:24:06.396692029 +0200 @@ -1,3 +1,4 @@ +#!/bin/zsh # zsh configuration file for Gromacs diff --git a/gromacs-gmxdemo.patch b/gromacs-gmxdemo.patch index f146ab7..1e1c9cf 100644 --- a/gromacs-gmxdemo.patch +++ b/gromacs-gmxdemo.patch @@ -1,6 +1,6 @@ -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 +diff -up gromacs-4.5.4/share/tutor/gmxdemo/demo.orig gromacs-4.5.4/share/tutor/gmxdemo/demo +--- gromacs-4.5.4/share/tutor/gmxdemo/demo.orig 2011-03-04 13:10:43.000000000 +0200 ++++ gromacs-4.5.4/share/tutor/gmxdemo/demo 2011-03-23 15:30:14.004163534 +0200 @@ -58,10 +58,10 @@ cat << _EOF_ ----------------------------------------------------------------- Before we can start any simulation we need a molecular toplogy @@ -13,7 +13,7 @@ diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tuto +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 ) + GROMOS structure file ( .gro extension ) @@ -72,22 +72,22 @@ _EOF_ if ( $?DISPLAY ) then @@ -45,7 +45,7 @@ diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tuto @@ -99,14 +99,14 @@ cat << _EOF_ ----------------------------------------------------------------- ----------------------------------------------------------------- - Because a simulation of a peptide in vacua is a bit unrealistic, we + Because a simulation of a peptide in vacuo 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. @@ -54,15 +54,15 @@ diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tuto -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 + 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. + right box size for our system. ----------------------------------------------------------------- -@@ -114,22 +114,22 @@ right boxsize for our system. +@@ -114,22 +114,22 @@ right box size for our system. _EOF_ if ( $?DISPLAY ) then @@ -93,19 +93,19 @@ diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tuto @@ -142,7 +142,7 @@ cat << _EOF_ ----------------------------------------------------------------- - In principle we can start a Molecular Dynamics simulation now. However + 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 + 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 + 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 ++the input files with the GROMACS preprocessor named g_grompp. 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 @@ -114,11 +114,11 @@ diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tuto if ( $?DISPLAY ) then - echo "The output of the grompp program should appear" -+ echo "The output of the g_g_grompp program should appear" ++ echo "The output of the g_grompp program should appear" echo "in a separate xterm window" endif -@@ -191,13 +191,13 @@ emtol = 1000.0 +@@ -190,13 +190,13 @@ emtol = 1000.0 emstep = 0.01 _EOF_ @@ -136,7 +136,7 @@ diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tuto echo -n "Press " set ans = $< -@@ -210,8 +210,8 @@ cat << _EOF_ +@@ -209,8 +209,8 @@ cat << _EOF_ ----------------------------------------------------------------- Now the binary topology file is generated, we can start the energy minimisation (EM). The program which performs the EM is called @@ -145,9 +145,9 @@ diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tuto +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 + 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 +@@ -223,21 +223,21 @@ rapidly drops down, and converges, to a _EOF_ if ( $?DISPLAY ) then @@ -174,25 +174,25 @@ diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tuto echo -n "Press " set ans = $< -@@ -255,7 +255,7 @@ fixed. This is called position restraine +@@ -254,7 +254,7 @@ fixed. This is called position restraine - Position Restrained MD keeps the peptide fixed and lets all water + 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. +-etc. that were not filled by the genbox program. ++etc. that 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. ) +@@ -273,7 +273,7 @@ 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 "The output of the g_grompp program should appear" echo "in a separate xterm window" endif -@@ -318,12 +318,12 @@ gen_seed = 173529 +@@ -317,12 +317,12 @@ gen_seed = 173529 _EOF_ @@ -209,7 +209,7 @@ diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tuto echo -n "Press " set ans = $< -@@ -346,19 +346,19 @@ _EOF_ +@@ -345,19 +345,19 @@ _EOF_ if ( $?DISPLAY ) then echo "Because your DISPLAY variable is set, I will pop up a" @@ -234,25 +234,25 @@ diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tuto echo -n "Press " set ans = $< -@@ -371,7 +371,7 @@ cat << _EOF_ +@@ -370,7 +370,7 @@ cat << _EOF_ ----------------------------------------------------------------- - Now our complete system is finally ready for the actual Molecular - Dynamics simulation. We start again by preprocessing the input files + 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 ++by the g_grompp program to generate the binary topology file (.tpb/.tpr extension). ----------------------------------------------------------------- -@@ -379,7 +379,7 @@ extension). +@@ -378,7 +378,7 @@ extension). _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 "The output of the g_grompp program should appear" echo "in a separate xterm window" endif -@@ -419,13 +419,13 @@ gen_temp = 300.0 +@@ -418,13 +418,13 @@ gen_temp = 300.0 gen_seed = 173529 _EOF_ @@ -270,7 +270,7 @@ diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tuto echo -n "Press " set ans = $< -@@ -444,20 +444,20 @@ increasing ( the total number of steps i +@@ -443,20 +443,20 @@ increasing ( the total number of steps i _EOF_ if ( $?DISPLAY ) then @@ -296,8 +296,8 @@ diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tuto echo -n "Press " set ans = $< -@@ -472,10 +472,10 @@ We are finished simulating, and we are g - trajectory. The trajectory file ( .trj extension ) contains all +@@ -471,10 +471,10 @@ We are finished simulating, and we are g + trajectory. The trajectory file ( .trr 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 @@ -309,7 +309,7 @@ diff -up gromacs-4.5.2/share/tutor/gmxdemo/demo.gmxdemo gromacs-4.5.2/share/tuto buttons to view your trajectory. 1. Once the program has been started a dialog box shows up. Click on -@@ -497,7 +497,7 @@ _EOF_ +@@ -496,7 +496,7 @@ _EOF_ if ( $?DISPLAY ) then echo Starting Trajectory viewer... diff --git a/gromacs.spec b/gromacs.spec index b4fae87..d3ba077 100644 --- a/gromacs.spec +++ b/gromacs.spec @@ -5,16 +5,17 @@ %endif Name: gromacs -Version: 4.5.3 -Release: 4%{?dist} +Version: 4.5.4 +Release: 1%{?dist} Summary: Fast, Free and Flexible Molecular Dynamics Group: Applications/Engineering License: GPLv2+ URL: http://www.gromacs.org BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) Source0: ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz -# File gotten from http://www.gromacs.org/@api/deki/files/126/=gromacs_manual-4.5.pdf -Source1: manual-4.5.pdf +# File gotten from +# http://www.gromacs.org/@api/deki/files/152/=manual-4.5.4.pdf +Source1: manual-4.5.4.pdf Source2: gromacs-template-makefile-single Source3: gromacs-template-makefile-double Source4: gromacs-template-makefile-mpi-single @@ -516,7 +517,7 @@ rm -rf %{buildroot} %files common %defattr(-,root,root,-) -%doc AUTHORS COPYING README manual-4.5.pdf README.fedora +%doc AUTHORS COPYING README manual-4.5.4.pdf README.fedora %{_bindir}/GMXRC %{_bindir}/GMXRC.bash %{_mandir}/man1/* @@ -597,6 +598,9 @@ rm -rf %{buildroot} %changelog +* Wed Mar 23 2011 Jussi Lehtola - 4.5.4-1 +- Update to 4.5.4. + * Sun Feb 13 2011 Jussi Lehtola - 4.5.3-4 - Get rid of executable stacks. diff --git a/sources b/sources index 991099e..ba69383 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -d5911585cd0e0b996dbbdcfb4c3bcf6b gromacs-4.5.3.tar.gz -0f6d3967f2d8fba5c5668f99dfc6aed7 manual-4.5.pdf +5013de941017e014b92d41f82c7e86d6 gromacs-4.5.4.tar.gz +1d4f96c5082e81740e1aa481c13f1537 manual-4.5.4.pdf