How to analyze gmx analysis in PBS queueing cluster

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1

GROMACS version: 2019.4
GROMACS modification: No
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Hi all,

I want to do gromacs analysis such as rmsd in a PBS queueing cluster. As you know, user should select 2 groups for rmsd calculation. How to include my favorite groups numbers in *.pbs file?

2

Hi,

You probably use a script to submit to the queue system. Depending to the shell that you use you can provide the numbers in the script. For example using
echo A B | gmx rmsd -f …
where a A = first number and B= second number

Best regards
Alessandra

3

Dear Alessandra,

Thanks for your answer.

My script for queue system is as follows:

#!/bin/bash
#PBS -P MATS1306
#PBS -N analysis
#PBS -l select=1:ncpus=24:mpiprocs=24
#PBS -l walltime=96:00:00
#PBS -q smp
#PBS -m be
#PBS -M
#PBS -r n
#PBS -o
#PBS -e
#PBS

module purge
module add chpc/gromacs/2019.4/openmpi-3.1.0/gcc-6.1.0
ulimit -s unlimited
OMP_NUM_THREADS=1

EXE=/apps/chpc/chem/gromacs/2019.4/bin/gmx_mpi
ARGS=“rms -f npt.xtc -s md.tpr -o rmsd.xvg -n index.ndx”

mpirun -np 24 {EXE} {ARGS}
popd

Based on your guidance, I used following cases, but I encountered with error:
1)
EXE=/apps/chpc/chem/gromacs/2019.4/bin/gmx_mpi
ARGS=“rms -f npt.xtc -s md.tpr -o rmsd.xvg -n index.ndx | echo 3 3”

EXE=/apps/chpc/chem/gromacs/2019.4/bin/gmx_mpi
ARGS=“echo 3 3 | rms -f npt.xtc -s md.tpr -o rmsd.xvg -n index.ndx”

EXE=/apps/chpc/chem/gromacs/2019.4/bin/gmx_mpi
ARGS=“rms echo 3 3 | -f npt.xtc -s md.tpr -o rmsd.xvg -n index.ndx”

How to resolve this issue?

Best,
Lilian

4