Computing interaction energies in namd

From: Samy Hamdouche (
Date: Tue Feb 22 2011 - 14:40:31 CST

I would like to compute the interaction energy between 4 atoms in a protein,
but I would like to do this for several different 4-atom clusters in the
protein. Within NAMD, the variable pairInteraction allows one to do this
given a PDB file with a flag for the desired four atoms. I.e.,
pairInteraction on
pairInteractionGroup1 1
pairInteractionFile namd-temp.pdb
pairInteractionSelf on
However, for the number of four-atom groups for which I would like to
compute interaction energies (15,000), it would be unfeasible to create
15,000 separate pdb files and read each one of them in the namd script. Is
there a simple way to compute interaction energies between given atoms in
namd where I can perhaps loop through all groups of atoms and print out the
within-group interaction energies for each group without creating 15,000
separate pdb files? I thought about just having 15000 different flags (1 for
each group), but this wouldn't work because many of the atoms are in
multiple groups. Thank you for your help,

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:19:51 CST