[gmx-users] How to visualizing gro file in pymol

Dries Van Rompaey dries.vanrompaey at gmail.com
Wed Feb 3 11:39:04 CET 2016


Your tpr file only has information on the starting configuration (because
it's a file that stores everything you need to start your simulation, not a
file that contains your output). Your end point .gro file can be converted
into a pdb through editconf as well.

However, a better approach would be to visualise your trajectory (.trr or
.xtc) using trjconv (http://manual.gromacs.org/programs/gmx-trjconv.html).

Kind regards


On 3 February 2016 at 11:33, anu chandra <anu80125 at gmail.com> wrote:

> Hello all,
> I just finished a short simulation of a membrane protein system and trying
> to visualize the final gro file generated from the simulation using Pymol.
> Unfortunately, the Pymol failed to visualize the protein in cartoon
> representation. Though VMD can do the job, I just wonder is there a way I
> can visualize the gro file in Pymol. A quick surfing on web suggested to
> use the editconf to convert the .tpr file to .pdb file for visualizing with
> Pymol. Unfortunately, here the .tpr file have structural information from
> the beginning of the simulation rather than at the end of the simulation.
> Any suggestion would be very much appreciated.
> Many thanks
> Anu
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