Documentos de Académico
Documentos de Profesional
Documentos de Cultura
http://chembytes.wikidot.com/gromacs-wiki 2010/10/31
Gromacs explained - Chembytes Page 2 of 7
Obtaining GROMACS
Watchers
GROMACS is a versatile package to perform molecular
AndreaMinoia dynamics, i.e. simulate the Newtonian equations of
motion for systems with hundreds to millions of
Watch: site | category | particles.
page It is primarily designed for biochemical molecules like
proteins, lipids and nucleic acids that have a lot of
This site is complicated bonded interactions, but since GROMACS
is extremely fast at calculating the nonbonded
Coffeeware interactions (that usually dominate simulations) many
groups are also using it for research on non-biological
systems, e.g. polymers. (From GROMACS wiki)
Care to help maintaining
You can download GROMACS here.
Chembytes? send over a th
Today (December, 7 2009) version 4.0.7 was
buck or two or disable your
release. Gromacs
ads blocker for this site, if
you have one. Thank you. (top)
(top)
• AMBER
• CHARMM
• COARSE GRAINING FORCE FIELS
• GROMOS
• OPLS
(top)
http://chembytes.wikidot.com/gromacs-wiki 2010/10/31
Gromacs explained - Chembytes Page 3 of 7
./configure --prefix=/home/user/gmx
./make
./make install
(top)
1. Serial version
#!/bin/bash
#$ -l virtual_free=4G
http://chembytes.wikidot.com/gromacs-wiki 2010/10/31
Gromacs explained - Chembytes Page 4 of 7
#$ -l h_cpu=00:10:00
#$ -N gromacs
2. Parallel version
#!/bin/bash
#$ -l virtual_free=4G
#$ -l h_cpu=00:10:00
#$ -pe gromacs_smp 2
#$ -N gromacs
1. Serial version
#!/bin/bash
#PBS -l nodes=1:ppn=1,walltime=50:00:00,mem=
#PBS -M your_mail_address
# Send me mail when job begins end and aborts
#PBS -m bea
#PBS -N jobname
cd /scratch
cd $PBS_O_WORKDIR
cp $tpr.tpr /scratch/$dirname
cd /scratch/$dirname
# execute mdrun
~/software/gmx4.0.7/bin/mdrun -s $tpr.tpr -de
(top)
http://chembytes.wikidot.com/gromacs-wiki 2010/10/31
Gromacs explained - Chembytes Page 5 of 7
(top)
#!/bin/bash
# This script is used to safately clean up th
# stored in a directory. If ' * ' is detected
# of files to remove, the script will die wit
# any file. This is convenient when working w
# directories and files.
# Author: Andrea Minoia
# Mail: minoiaa@gmail.com / http://chembytes.
http://chembytes.wikidot.com/gromacs-wiki 2010/10/31
Gromacs explained - Chembytes Page 6 of 7
rm -f $@
(top)
Comments
Add a New Comment
C++
C++ Experts are Ready to Help. Join Now for Free.
CFanatic.com/CPlusPlus-Programming
http://chembytes.wikidot.com/gromacs-wiki 2010/10/31
Gromacs explained - Chembytes Page 7 of 7
Unless otherwise stated, the content of this page is licensed under Creative Commons
Attribution-ShareAlike 3.0 License
http://chembytes.wikidot.com/gromacs-wiki 2010/10/31