RE: water-protein interation

From: Hongbo Du (
Date: Fri Nov 14 2014 - 09:03:37 CST

Hi, Yeping,

Please check the following link. You can read out the velocity, mass of each atom you are interested in, e.g. some amino acid residues in your simulation system. If you combine the time step you are using, you can obtain the force applying on the atoms of each residue. If you just want to get the force induced from solvent, I don't have a good idea. However, you can calculate the pair interactions between the solvent and the specific residue to reach the non-bonded energy terms. For the pair interaction calculation, please check the manual.

Good luck.


From: [] on behalf of sunyeping []
Sent: Friday, November 14, 2014 2:32 AM
To: namd-l
Subject: namd-l: water-protein interation

Dear all,

Do you have any idea how to analyze the interaction force imposed by the solvent on a particlular reside in the protein in MD simulation?

Best regards.

Yeping Sun

Institute of Microbiology, Chinese Academy of Sciences

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