energy groups in NAMD

From: Andre Ribeiro (
Date: Fri Mar 06 2015 - 14:22:34 CST


I have essentially no experience with NAMD, so I apologize if there are
trivial answers to some parts of my question.

I have been developing a method for analyzing MD simulations based on
protein energy networks ( A
requirement for the method is to calculate inter-residue interaction
energies. I have established a protocol for doing the required steps with
another simulation package, but I would like to extend this functionality
for NAMD as well.

>From what I was able to find out, interaction energies can only be
calculated for a single pair of energy groups at a time:

At this point I should note that writing an external script for
defining/performing this calculation several times for different energy
groups is not feasible for my objectives. As I was not able to find a
standard solution to my problem, I started to check the source code.

The file ComputeNonbondedBase2.h seems to perform the corresponding
calculations, and storing the contributions to nonbonded energies in a
matrix would solve my problem. However, I haven't been able to figure out a
way to access the global atom numbers within this block of code. The
indices i and j seem to be local to a subset of the atoms of the system. I
need to access the global atom numbers, so I can correctly classify atoms i
and j as belonging to one of the energy groups being analyzed.

I would really appreciate any suggestions on how to do this.

Thank you,
Andre Ribeiro
Columbia University

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