Re: Computing interaction energies in namd

From: JC Gumbart (
Date: Tue Feb 22 2011 - 14:48:51 CST

Use the NAMDEnergy plugin in VMD. You'll find it's very amenable to scripting.

On Feb 22, 2011, at 2:40 PM, Samy Hamdouche wrote:

> Hello,
> I would like to compute the interaction energy between 4 atoms in a protein, but I would like to do this for several different 4-atom clusters in the protein. Within NAMD, the variable pairInteraction allows one to do this given a PDB file with a flag for the desired four atoms. I.e.,
> pairInteraction on
> pairInteractionGroup1 1
> pairInteractionFile namd-temp.pdb
> pairInteractionSelf on
> However, for the number of four-atom groups for which I would like to compute interaction energies (15,000), it would be unfeasible to create 15,000 separate pdb files and read each one of them in the namd script. Is there a simple way to compute interaction energies between given atoms in namd where I can perhaps loop through all groups of atoms and print out the within-group interaction energies for each group without creating 15,000 separate pdb files? I thought about just having 15000 different flags (1 for each group), but this wouldn't work because many of the atoms are in multiple groups. Thank you for your help,
> Samy

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