VMD-L Mailing List

From: Daipayan Sarkar (sdaipayan_at_gmail.com)
Date: Thu Aug 31 2023 - 03:00:20 CDT

Hi,

Are you sure the molecule is built correctly? Said differently, this could easily be due to your psfgen script where I assume you have topology files for the molecule you are working with. For that more specific information about the molecule would be necessary. This is of course if you are planning to simulate the molecule.

“i need the reduce their length to a specific value” - I personally do not recommend, even if you are using VMD only for visualization purposes.

-Daipayan

From: "owner-vmd-l_at_ks.uiuc.edu" <owner-vmd-l_at_ks.uiuc.edu> on behalf of maxim todoru <mtodoru_at_gmail.com>
Date: Thursday, August 31, 2023 at 3:35 AM
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: How to shortening bonds length in a molecule ?

Hi VMD community,
I used VMD to perform the visualisation of some organic molecules, but it appears that some bonds length are little tall from normal, and i need the reduce their length to a specific value. I failed to figure out a solution, and i need some help.