From: Roshan Shrestha (roshanpra_at_gmail.com)
Date: Mon Jun 27 2022 - 08:47:31 CDT

Hi,
     As others have suggested, you can use the distance cut-off in VMD to
visualize these CG bonds. However, there is also a small kind of hack that
you can do, which I guess is explained in one of the Martini tutorials.

$ gmx trjconv -f equilibration.gro -s dynamic.tpr -pbc whole -o
equilibration.pdb -conect
Select System in this step. Then:
$ sed "/ENDMDL/d" -i equilibration.pdb
$ vmd equilibration.pdb viz.xtc

Now, you can visualize your CG bonds in VMD. Thanks.

With best regards

On Mon, Jun 27, 2022 at 3:36 PM Vermaas, Josh <vermaasj_at_msu.edu> wrote:

> If you implicitly trust what is in the tpr file, and don’t mind
> recompiling VMD, there is also https://urldefense.com/v3/__https://github.com/jvermaas/vmd-tprreader__;!!DZ3fjg!6a-4LVOyPkNl6JDcXd38xjRa95OSi_sPGf1BoyieEnUEUIik9nWnEXIDzcjrQnkoriPLcA6TPYSn027iH50$
> <https://urldefense.com/v3/__https://github.com/jvermaas/vmd-tprreader__;!!DZ3fjg!7aSXUbrIw_xov2Ovb09kW90HuPo0Drna3fAi21D4UaxzHtzI0BQS5e_mgbhct5MYpQxwr9Ov5nRGRKW3wBk$>,
> which will read the definitions from the tpr file. I have not checked if
> GROMACS 2022 changed the tpr generator (again) or not in a way that breaks
> the tpr reader.
>
>
>
> -Josh
>
>
>
> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of "Smith, Harper E." <
> smith.12510_at_buckeyemail.osu.edu>
> *Date: *Sunday, June 26, 2022 at 7:58 PM
> *To: *Raman Preet Singh <ramanpreetsingh_at_hotmail.com>, "vmd-l_at_ks.uiuc.edu"
> <vmd-l_at_ks.uiuc.edu>
> *Subject: *vmd-l: Re: Visualisation of CG bonds
>
>
>
> 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
>
>
>
>
>

-- 
*Roshan Shrestha*
PhD Student
MOBI team
Molecular Microbiology and Structural Biochemistry (MMSB) - UMR5086
Institut de Biologie et Chimie des Protéines (IBCP)
7 passage du Vercors
69367 LYON Cedex 07