From: Mersch, Kacey (
Date: Thu Oct 22 2020 - 15:30:16 CDT

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!
From: Mersch, Kacey
Sent: Thursday, October 22, 2020 2:40 PM
To: <>
Subject: Pair Interaction Calculation

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


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