VMD-L Mailing List
From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Apr 24 2019 - 15:39:47 CDT
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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 http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/
-Josh
On 2019-04-24 12:42:44-06:00 owner-vmd-l_at_ks.uiuc.edu 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<http://www.chem.utoronto.ca/wp/jockusch/>, U of T
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