Run Gromacs to generate outputs.
mpirun -np 64 -x UCX_NET_DEVICES=mlx5_0:1 mdrun_mpi -v -s stmv.tpr -nsteps 10000 -nb cpu -pin on
Above step should generate “confout.gro” file which we will be using to display.
Install VMD on Windows or Linux system from https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD.
Execute VMD
Load confout.gro from Molecule File Browser Window.
It should open a display Window like below.
Now, we want to visualize only Protein.
In the VMD main window, choose Graphics → Representations.
In the Graphical Representations window, choose Selections, click the Reset button, double click “protein” from Singlewords section and click Apply button.
Now, it should display only Protein in VMD display like below.
More VMD tutorial is available at https://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node2.html.
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