[gmx-users] (no subject)

[Justin Lemkul]

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
>

-- 
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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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