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
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