Re: How to replace NAMD electrostatics

From: Axel Kohlmeyer (
Date: Tue Nov 19 2013 - 16:53:01 CST

On Tue, Nov 19, 2013 at 11:36 PM, Juba, Derek <> wrote:
> Hi, I'm interested in replacing NAMD's electrostatic calculations with some
> of my own, and was wondering if anyone could give me some advice on how to
> do this. As far as I can tell, the simplest way would be to set the cutoff
> parameter for nonbonded interactions to a distance of 0, and then use the
> extForces parameter to call my program to perform my electrostatic
> calculations, and then add the resulting forces to NAMD's other forces.

i don't think that will work. you will have to rewrite the source code.

> One trouble with this is that it would disable NAMD's Van der Waals
> calculations in addition to the electrostatics, but I think I could
> calculate the Van der Waals forces myself as well without too much trouble.

at this point you already have pretty much written your own MD code.

> My questions are, first, will this work for disabling NAMD's electrostatics,
> or is there some gotcha that I'm missing? And second, is there a better

how about exclusions?

> way, that might allow NAMD to continue to perform the Van der Waals
> calculations?

there are a lot of issues with your approach. i wonder which feature
of NAMD it is that makes you desire to modify it rather than writing
your own MD code? based on the information you provide, you may be
better off looking for an MD code, which is designed to allow people
to easily replace potentials.


> Thanks for any help,
> -Derek Juba

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:55 CST