[gmx-users] Loading topology into vmd

[Miro Astore]

This is very helpful thank you. I think I can use this. I will also ask the
vmd mail list.

Best, Miro

Le mer. 15 janv. 2020 à 19:35, Alessandra Villa <
alessandra.villa.biosim at gmail.com> a écrit :

> 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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