Computing several pair interactions

From: Samy Hamdouche (
Date: Tue Feb 15 2011 - 18:11:25 CST

I would like to compute the within-group interaction energies of several
4-atom groups in a protein. Within NAMD, the variable pairInteraction allows
one to do this given a PDB file with a flag for the desired four atoms.
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,

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