From: Josh Vermaas (
Date: Mon Oct 26 2020 - 18:21:20 CDT

Hi Kacey,

I think we need to back up a bit here. Energies in MD come from the
potentials defined in the forcefield, while the forces are just based on
the gradient of the potential energy function. The VDW and electrostatic
potentials are pairwise between atoms in the CHARMM force field you are
using, meaning that every pair of atoms not otherwise excluded (eg.
connected through bonds, or are further than the cutoff distance apart)
contributes to the sum of elec and VDW energies. The pair interaction
calculation follows the same logic, except that instead of doing the
calculation for every possible pair, you only do so for atom pairs where
one element from the pair is in pairInteractionGroup1, and the other
element is in pairInteractionGroup2. Due to this limitation,
pairInteraction calculations are only useful for analysis after simulation
(or on static structures), since the dynamics using that option are all
kinds of wrong for obvious reasons.


On Mon, Oct 26, 2020 at 3:35 PM 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

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