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Run Gromacs to generate outputs.

mpirun -np 40 -x UCX_NET_DEVICES=mlx5_0:1 -bind-to core -report-bindings \
mdrun_mpi -v -s stmv.tpr -nsteps 10000 -nb cpu -pin on

Above step should generate “confout.gro” file which we will use to visualize.

Install VMD on Windows or Linux system from https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD.

Visualizing confout.gro usingVMD

Execute VMD

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