VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Mon Jun 27 2022 - 07:52:11 CDT

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!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