**From:** Andre Ribeiro (*aar2163_at_gmail.com*)

**Date:** Fri Mar 06 2015 - 14:22:34 CST

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Hi,

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 (http://pubs.acs.org/doi/abs/10.1021/ct400977r). 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:

http://www.ks.uiuc.edu/Research/namd/2.10/ug/node75.html

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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