Run Gromacs to generate outputs.
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mpirun -np 4064 -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 be using to visualizedisplay.
Install VMD on Windows or Linux system from https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD.
Execute VMD
Visualizing Load confout.gro usingVMD
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from Molecule File Browser Window.
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It should open a display Window like below.
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Now, we want to visualize only Protein.
In the VMD main window, choose Graphics → Representations.
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In the Graphical Representations window, choose Selections, click the Reset button, double click “protein” from Singlewords section and click Apply button.
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Now, it should display only Protein in VMD display like below.
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More VMD tutorial is available at https://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node2.html.