[gmx-users] how to visualize gromacs trajectory

[Sun Yeping]

Dear all,

I wish to know what is the best way to visualize gromacs trajectory.

When I load a gromacs trajectory into VMD, I find some of the water
molecules and some part of the protein in the system are streched and the
structure become weild and cannot be properly analyzed.

I searched google and found there is a gromacs plugin for vmd, but I don't
know whether it will help improve gromcas trajectory visualization (
https://www.ks.uiuc.edu/Research/vmd/plugins/updates/vmd192_gromacs_update1/
).

I also found there is a gromcas plugin for pymol (
https://bioexcel.eu/run-gromacs-within-pymol-with-dynamics/). But it seems
to be used for simulation. It doesn't seem to be used to load and visualize
a extraneous the gromacs trajectory.

What are your suggestion？ Thank you in advance.

Yeping