Handling of nonbonded lists in PSF - please clarify

From: Randy J. Zauhar (r.zauhar_at_usciences.edu)
Date: Sun Feb 25 2018 - 14:42:10 CST

Hi Jerome,

Referring back to this question :


Could you please clarify your response regarding the format of the nonbonded exclusion list? In particular could you modify that for the case :

8 atoms total

atoms 1 is unchanging
atoms 2-3 are final
atoms 4-6 are initial
atoms 7-8 are ‘unchanging

Looking at your alchemify code I would expect the first two lines to be

6 !NNB
2 3 2 3 2 3

corresponding to 3 copies of the 2 final atom indices, one set of final atoms to be assigned to each of the initial atoms.

According to the alchemify code (and an actual run on my own system) it seems the resulting ‘second section’ would look like this :

0 0 0 2 4 6 6 6

Here, the each of the eight atoms is assigned an offset of some sort into the exclusion lists.

The atoms before the first ‘initial’ atom have 0 offset into the list - does that mean the list is being ignored, or it’s being used and we start at position 0 (i.e. atoms 2 & 3)?

The first initial atom has offset 2, which means what? Do we skip the first set of two atoms in the exclusion list? In any event, I guess this implies it cannot see atoms 2 and 3, which makes sense.

The last ‘initial’ atom gets an offset of 6, meaning what? By my interpretation above that would be off the end of the list of exclusions. And that setting continues for all the remaining atoms.

The mind reels. I will assume there is some logic in NAMD under which all this makes sense.

The reason I am asking - I was not able to get my ‘mixed’ simulation with site solvent as ‘final’ atom set and ligand as ‘initial’ atom set to work, it blows up with nonbonded interactions clearly not being excluded. I have tried using FEP but with fixed lambda, and without FEP by using an ‘alchemified’ PSF, and in both cases the same bad result. I am trying to troubleshoot.



Randy J. Zauhar, PhD

Prof. of Biochemistry

Dept. of Chemistry & Biochemistry
University of the Sciences in Philadelphia
600 S. 43rd Street
Philadelphia, PA 19104

Phone: (215)596-8691
FAX: (215)596-8543
E-mail: r.zauhar_at_usciences.edu<mailto:r.zauhar_at_usciences.edu>

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