Re: How to replace NAMD Eletrostatic Forces

From: Brian Radak (
Date: Thu Aug 04 2016 - 15:17:17 CDT

1.) I'm not sure you can turn off the computation of electrostatics
completely, but using "PME off" should bypass a lot of the computational
cost. You can turn off the effect of electrostatics in a number of ways,
for example by zeroing the charges or just using "nonbondedscaling 0",
but the latter also turns of LJ interactions I believe.

2.) TclForces is a good sandbox for trying new models, but I wouldn't
necessarily recommend it for production runs of something like brute
force protein folding.

If you are doing pairwise potentials, you can also try using the
tabulated non-bonded interactions, but these might not be well-typed for
what you want.

Unfortunately (fortunately?) the main purpose of NAMD is exactly to
accelerate the electrostatics, so those routines are a pretty essential
and central part of normal execution. You'd have to tell use more about
what kinds of models you want to use to get more specific advice.


On 08/04/2016 01:15 PM, Emerson Macedo wrote:
> Hello NAMD experts!!
> I am new with NAMD and currently working on
> adapt it to our research with proteing folding simulations.
> My current challenge involves the possibility of using our
> implementation of electrostatic force calculations instead of NAMD's
> version.
> My first thought was (naive I guess) find a way to
> disable NAMD version and then add out implementation.
> Here my questions:
> 1) How does one could disable NAMD electrostatic calculations or
> replace them?
> 2) Does it make sense to use TCLForces API to implement our version or
> would be
> better to implement directly in the source code?
> Any directions would be very much appreciated.
> Thank you all for any help.
> My best regards,
> Emerson

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

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