Re: Computing interaction energies in namd

From: Jérôme Hénin (
Date: Wed Feb 23 2011 - 03:42:14 CST


To me it sounds like you are trying to push NAMD through a
GROMACS-shaped hole. Computing lots of interaction energies is a very
GROMACSian idea, if I remember well. Maybe you'd be better off using
that code? In principle it can evaluate the CHARMM force-field,
although when I tried a while ago, I could not get exact results.


On 23 February 2011 02:07, Axel Kohlmeyer <> wrote:
> On Tue, Feb 22, 2011 at 7:21 PM, Samy Hamdouche <> wrote:
>> 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,
> why trying to make a 10 ton elephant like namd jump through hoops?
> it would probably be easier to write a custom "pseudo MD" code that
> just loops over the interaction tuples that you want. there are plenty
> of "toy" MD codes around that can be adapted for that. at least that
> is what i would suggest based on the very limited information about
> your objective that you provide.
> the next best thing would be to hack NAMD yourself, but i would
> guess that it would take you longer.
> axel.
>> Samy
>> 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
> --
> Dr. Axel Kohlmeyer
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.

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