Hi,

(1) GROMACS is installed in /usr/local/gromacs/bin/

Not in root as I mentioned earlier.

(2) When I gave

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -N smp1
#$ -l h_vmem=1G
usr/local/gromacs/bin/gmx mdrun -ntmpi 1 -ntomp 8 -v -deffnm eq

I got the same error again.

But, when I run it directly my login node,   gmx mdrun -ntmpi 1 -ntomp 8 -v
-deffnm eq the command works fine.


I realize, the problem lies in my scripiting. How to fix it? Is there any
special method to set the path in the above submit.sh file?

Executable:   /usr/local/gromacs/bin/gmx
Library dir:  /usr/local/gromacs/share/gromacs/top


Can anyone help me?

Thanks,
Subashini.K
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