Re: pairInteraction commands

From: Brian Radak (
Date: Mon Feb 20 2017 - 08:19:54 CST


Is this not well described in the manual? Numerous options use flags
from a PDB file, usually from the occupancy (O) or B-factor (B) columns,
sometimes one or the other by default and sometimes defaulting to the
coordinate PDB (even if those coordinates are overwritten by binary or
trajectory coordinates, the other columns can still be used).

My loose remembrance from the source code is that pairInteraction sets
groups based on 1 and -1 flags, much like the alchemy keyword.


On 02/19/2017 04:39 PM, matthew reeves wrote:
> 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
> Matthew

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643

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