[gmx-users] Loading topology into vmd

[Miro Astore]

Hi kenny, thanks for getting back to me.

I use something similar to what you've suggested to deal with periodic
boundary conditions. My current issue is that vmd will place a bond between
two atoms that are close together in the first frame of the visualization
even if those atoms aren't linked in the topology. The fake bonds are then
kept throughout the visualization . That is, when I load just a gro and a
trr.

A psf file would fix this situation but my efforts to recreate a whole one
from my complex system using top2psf.pl hasn't borne much fruit.

Just wondering what other people have tried.

Best, Miro

Le mer. 15 janv. 2020 à 02:20, Kenny Goossens <goossens_kenny at hotmail.com>
a écrit :

> 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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