understanding the lone pair section of psf files

From: Frank Haverkort (f.haverkort_at_rug.nl)
Date: Thu Aug 22 2013 - 10:44:17 CDT

I want to use the Charmm Drude polarizable force field for my MD
simulations, but do not have a license of the CHARMM program that is
needed to build input psf files. Instead, I'm using a combination of
NAMD's psfgen tool plus a self made script that adds the polarizability
on top of the non-Drude psf file. In order to do this, I need to
understand what a Drude psf file should look like, but I don't
understand its NUMLP section that describes the lone pairs.

I've obtained a sample SWM4-NDP water psf from
http://www.ks.uiuc.edu/Research/Drude/, which describes the lone pairs
with the following lines:
        216 864 !NUMLP NUMLPH
          3 1 F -0.240345 0.00000 0.00000
          3 5 F -0.240345 0.00000 0.00000
          3 9 F -0.240345 0.00000 0.00000
          3 13 F -0.240345 0.00000 0.00000
          3 17 F -0.240345 0.00000 0.00000
etc.

I understand the 216 - the total number of lone pairs. But I don't know
what is the information conveyed by the column of 3's, the column of
-0.240345's, and probably most importantly, the column
1
5
9
13

In my simulation the water molecules will have different numbers than in
this sample, and I don't know how to modify this column for my case
because I don't understand what the numbers stand for.

I'd be grateful if any of you could offer some clarification.

The best,
Frank

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:33 CST