pairInteraction commands

From: matthew reeves (
Date: Sun Feb 19 2017 - 16:39:27 CST

Hi all,

I’ve been trying to calculate the interaction energy between 2 groups of atoms, I understand I need to use ‘pairInteraction’ and related commands in the configuration file.

This might seem like an odd question but would anyone mind explaining to me how I go about specifying which atoms in the PDB file are to be included in the calculation of the interaction energies? As this PDB file is usually different to that which provides the atomic coordinates. I’ve read through the tutorials and it only seems to give a brief explanation here.

Any help would be much appreciated.

Best Wishes

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