From: Jeff Comer (
Date: Mon Oct 26 2020 - 18:37:05 CDT

I think your question is a good one. I would just do the calculations
manually as you suggested. I typically take the trajectory from a
simulation and create 3 DCD files containing receptor+ligand, receptor
only, and ligand only. These can be run back through NAMD to calculate the
complex energy and self-interaction energies as you suggested to get E_bind
= E_receptor+ligand - E_ligand - E_receptor at each frame.

I agree that the documentation is not clear on what pairInteraction does.
This could probably be resolved by looking at the source code, but I don’t
see any reason for that since the manual method is easy.


On Mon, Oct 26, 2020 at 16:34 Mersch, Kacey <> wrote:

> I recently calculated the VDW Energies of one sidechain with many other
> sidechains individually on a static protein structure (no simulation was
> run) using the pair interaction calculation option. The values calculated
> are exactly the same as if I were to calculate them manually. With that in
> mind, what equation or process goes on when the pair interaction
> calculation is being performed?
> When performing the calculations manually, one would calculate the VDW
> energies in two sidechains and the interactions between them and then
> subtract away the self-interactions that occur between the atoms of each
> sidechain individually. This would leave you with only the VDW energies
> between the two sidechains.
> The manual states the outcome of using the pair interaction is the
> calculation of the energies between those two groups of flagged atoms. But,
> how is that calculated? is there a basic addition or subtraction process
> that occurs or something more complicated?
> initial config
> coordinates /VDW/17.pdb
> temperature 300K
> # output params
> outputname /VDW/
> binaryoutput yes
> # force field params
> structure /VDW/VDWDECOMP.psf
> parameters /VDW/par_all27_prot_lipid_na.inp
> paraTypeXplor off
> paraTypeCharmm on
> exclude scaled1-4
> 1-4scaling 1.0
> switching on
> switchdist 8.0
> cutoff 12.0
> pairlistdist 13.5
> stepspercycle 20
> pairInteraction on
> pairInteractionFile 17.pdb
> pairInteractionCol B
> pairInteractionGroup1 1
> pairInteractionGroup2 2
> One note for the question below. I am not asking about the calculations
> that occur when getting numbers for forces (VDW, ELEC). But, how those
> numbers are manipulated to get the energies between the two groups of
> atoms. So, my question is not about the LJ potential but, rather how does
> NAMD set aside the number calculated between the two groups of atoms.
> Any help is greatly appreciated!
> Kacey
> --

Jeffrey Comer, PhD
Associate Professor
Department of Anatomy and Physiology
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

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