[gmx-users] Loading topology into vmd

[Kenny Goossens]

Hi,

I'm not sure what you mean by "bonds that aren't in the simulation", but from my experience, converting your .gro file with gmx trjconv using the -pbc mol and -ur compact options usually gives a clean visualisation. If necessary, you can also use the -center option to center a specific structure/residue in the box. You can have the output written in the .gro file format, or convert to anything more convenient.

With kind regards,
______________________________
Kenneth Goossens, PhD student
Laboratory of Medicinal Chemistry (Building A - Room 2.13)
University of Antwerp - Campus Drie Eiken
Universiteitsplein 1
B-2610 Wilrijk
Belgium



________________________________
Van: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> namens Miro Astore <miro.astore at gmail.com>
Verzonden: dinsdag 14 januari 2020 3:48
Aan: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
Onderwerp: [gmx-users] Loading topology into vmd

Hello all,

I'm just wondering how people load topologies for systems simulated in
gromacs into vmd. It is very annoying to have bonds that aren't in the
simulation placed in the visualisation. I'm wondering if anyone has a
solution that is easier than simply creating a psf file of the .gro system
as this can be time consuming for systems with strange geometries.

Best, Miro
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