Re: Computing interaction energies in namd

From: Samy Hamdouche (
Date: Tue Feb 22 2011 - 18:21:46 CST

I've played around with the NAMDEnergy plugin of VMD. The problem with its
application in my case is that it's very slow when computing on the order of
10000 interaction energies, because it creates 10000 separated pdb files
with atom flags and runs a namd script with exactly the lines I quoted
originally. I was wondering if there was a quicker (perhaps lower level) way
of computing this many interaction energies within namd. Thanks,

On Tue, Feb 22, 2011 at 12:48 PM, JC Gumbart <> wrote:

> 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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