[gmx-users] Loading topology into vmd

Alessandra Villa alessandra.villa.biosim at gmail.com
Wed Jan 15 09:35:14 CET 2020


Hi,
One of the criteria that VMD uses to define bond is distance criteria. When
you source your gro file, this criteria is applied.
One way one, I have used is to not visualize  undesired bonds, is the
following:
delete the undesired bonds, save the vmd setting (*.vmd file),  load the
setting before any of the following visualizations.
That is not the most elegant way, but it works in my case.
For more elegant ways, you could ask to VMD maillist.
Best regards
Alessandra


On Tue, Jan 14, 2020 at 8:59 PM Miro Astore <miro.astore at gmail.com> wrote:

> 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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