Computing interaction energies in namd

From: Samy Hamdouche (rich.fish_at_gmail.com)
Date: Tue Feb 22 2011 - 14:40:31 CST

Hello,
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,
Samy

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