VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Jun 27 2022 - 09:41:15 CDT

In addition to that, if the topology of the system is fixed you SHOULD be
able to visualize it just fine as long as yu've loaded a file with the bond
information. If you have done so and the bonds don't appear, we'd need more
information on exactly what you tried and what errors you're seeing.
Best,
Peter

On Sun, Jun 26, 2022, 8:27 PM Smith, Harper E. <
smith.12510_at_buckeyemail.osu.edu> wrote:

> Hi Raman,
>
> You can use the "DynamicBonds" representation in VMD and change the
> distance cutoff.
>
> HTH,
> Harper
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Raman Preet Singh <ramanpreetsingh_at_hotmail.com>
> *Sent:* Sunday, June 26, 2022 2:07 PM
> *To:* vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> *Subject:* vmd-l: Visualisation of CG bonds
>
> Dear All, I have run a CG simulation in Gromacs using Martini FF and would
> like to visualise the trajectory in VMD. There's a Tcl script available on
> Martini website but that keeps on returning errors (with both, the .tpr
> file and the .top
> Dear All,
>
> I have run a CG simulation in Gromacs using Martini FF and would like to
> visualise the trajectory in VMD. There's a Tcl script available on Martini
> website but that keeps on returning errors (with both, the .tpr file and
> the .top file). The errors have been reported by others also but the fixed
> used by others have not worked in my case.
>
> As I understand,VMD draws bonds based on a distance based cutoff. I was
> wondering if there is a way to draw long bonds, as is typical in CG MD, in
> VMD. In case VMD can not do that, is there any other visualiser that can be
> of help.
>
> Regards,
> Raman
>
>
>