From: Vermaas, Joshua (
Date: Wed Apr 24 2019 - 15:39:47 CDT

Hi Neena,

The h-bond plugin can do this (Extensions->Analysis). By default it looks at all interactions over the whole system, but if you are super selective with your selections, it can zero in on a specific interaction. See


On 2019-04-24 12:42:44-06:00 wrote:

Hello VMD users,
How to track H-bonds at a particular location (say amide carbonyl of residue n) as a function of time from a MD trajectory using VMD? My goal is to understand the dynamics of H bonds at that particular location.
Many thanks,
Neena Eappen
Graduate Student
Jockusch Lab<>, U of T