Gromacs Visualization using VMD

This post will walk you through generating visualization of the Gromacs molecule.

In this example we will use STMV 1M atoms.

To get started, follow Get Started with Gromacs to build your Gromacs execution mdrun_mpi

1. Run Gromacs

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.

2. Install VMD

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

3. Visualize Gromacs

a. Execute VMD and load confout.gro in the Molecule File Browser Window.

It should open a display Window like below.

b. Filter the protein from the water.

In the VMD main window, choose Graphics → Representations.

c. 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.