From: Juba, Derek (derek.juba_at_nist.gov)
Date: Tue Nov 19 2013 - 16:36:20 CST
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.
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.
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 way, that might allow NAMD to continue to perform the Van der Waals calculations?
Thanks for any help,
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