Hello,
I am running a VMD simulation and using VMD software to analyze hydrogen bonds, but I want to study electrostatic interaction. I would like to have a graph number of bonds through time. I don't know if I'm in the right place to ask, but would you know how to obtain this graph for the electrostatic bond? I tried to find answers on the internet but couldn't find any.
Thank you so much for your help.
Alix
Hi Alix! I suspect that you use a trajectory from another MD engine to analyze with VMD, right? Because VMD is mainly a visualization tool. So if you want to analyze electrostatics with PME then you have to open Extensions-> Analysis and there you find PME electrostatics. In the same section you may find hydrogen bonds analysis. If you want to know if two particles with positive and negative charges can associate with each other then you might need to compute RDFs between chosen pairs of atoms. Otherwise, for looking for bonds I would probably suggest you to use another tool for analyzing your trajectory or to write your own customized.
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