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

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