On 8/2/12 10:09 AM, vidhya sankar wrote:
Dear Gromacs user , I Write Some linux .sh programming to automate
grompp and mdrun process in Clustering which is as Follows
Could Any one of you point out the error in following script files ? is it
correct or not.
Are you getting an error message? If so, what is it? Why are you using
-maxwarn with grompp? There's rarely a good reason to do so.
There's also no reason to redefine environment variables if their values are not
changed, so you can save yourself a few lines.
-Justin
#!/bin/bash
#! -l nodes=1:ppn=4
# load the modules
# preproc
source="/usr/local/plumedmpigromacs/bin"
GROMPP="/usr/local/plumedmpigromacs/bin/grompp_mpi_d"
MDRUN="/usr/local/plumedmpigromacs/bin/mdrun_mpi_d"
$GROMPP -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index0.ndx -o 232npt0.tpr
-maxwarn 1 -po mdout0.mdp &>/dev/null
mpirun -np 4 $MDRUN -deffnm 232npt0 -cpi 232npt0_prev.cpt &>/dev/null
#exit
# preproc
source="/usr/local/plumedmpigromacs/bin"
GROMPP="/usr/local/plumedmpigromacs/bin/grompp_mpi_d"
MDRUN="/usr/local/plumedmpigromacs/bin/mdrun_mpi_d"
$GROMPP -f npt_umbrella.mdp -c conf153.gro -p topol.top -n index153.ndx -o
232npt153.tpr -maxwarn 1 -po mdout153.mdp &>/dev/null
mpirun -np 4 $MDRUN -deffnm 232npt153 &>/dev/null
#exit
Thanks in Advance
With Regards
S. Vidhya sankar
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
