[gmx-users] Problems when loading .trr and/or .trj GROMACS trajectory files in VMD?

Mark Abraham mark.j.abraham at gmail.com
Wed Mar 26 17:21:30 CET 2014

The standard VMD workflow is to load a file that either contains a
molecular topology, or permits VMD to infer one (e.g. PDB or GRO generally
do the latter). Then you import trajectory coordinates into that.
Trajectory formats like .trr do not have enough information for VMD to do
sensible guessing if you manage to load them on their own.


On Wed, Mar 26, 2014 at 4:34 PM, Juan Munoz-Garcia <
juan.munoz-garcia at bioch.ox.ac.uk> wrote:

> I'm a new GROMCAS user. I've run an NVT equilibration of a explicitly
> solvated protein-ligand complex, I've extracted frames throughout the
> trajectory in both .pdb and .gro format and I've open them in VMD and I've
> checked the simulation's gone fine . However, when I try to open in VMD
> either the .trr or .trj trajectory file just the water box appears (as
> white single-point dots, not the whole water molecule) but not the protein
> or ligand. Have any of you experienced this issue before? Could it be a
> problem of the .trr/.trj VMD plugins? I'd really appreciate you
> commentaries.
> Thank you.
> Regards.
> Juan C. Munoz-Garcia, PhD
> Biomembrane Structure Unit
> University of Oxford
> South Parks Road
> Oxford OX1 3QU
> juan.munoz-garcia at bioch.ox.ac.uk
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list