From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Nov 19 2013 - 17:00:16 CST
you may want to consider OpenMM, in particular search the documentation for
"CustomNonBondedForce" and "CustomCompoundBondForce".
the above will make adding your own custom potential extremely easy. I'm
not sure how easy it is to disable the electrostatics though, you might
still need to follow Axel's suggestion of just setting the charges to 0
(though sadly this means the calculations still take place).
On Tue, Nov 19, 2013 at 5:54 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Tue, Nov 19, 2013 at 11:36 PM, Juba, Derek <derek.juba_at_nist.gov> wrote:
> > Hi, I'm interested in replacing NAMD's electrostatic calculations with
> > of my own, and was wondering if anyone could give me some advice on how
> > do this. As far as I can tell, the simplest way would be to set the
> > 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.
> > 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
> > My questions are, first, will this work for disabling NAMD's
> > or is there some gotcha that I'm missing? And second, is there a better
> > way, that might allow NAMD to continue to perform the Van der Waals
> > calculations?
> i forgot this one. sure. there is an easier way, you can just set all
> charges to zero.
> > Thanks for any help,
> > -Derek Juba
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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