From: Hadi (dinpajooh_at_gmail.com)
Date: Fri Aug 23 2013 - 12:11:39 CDT
216: total number of lone pairs.
864: number of lone pair hosts in a host table.
column of 3: number of lone pair hosts.
column of F: A logic used during simulations.
column of -0.240345: the distance of lone pair from the oxygen atom in the
direction of the H1-H2 bisector.
column
1
5
9
13
..
Pointers used for lone pair hosts.
Good luck!
Hadi Dinpajooh
Arizona State University
On Thu, Aug 22, 2013 at 8:44 AM, Frank Haverkort <f.haverkort_at_rug.nl> wrote:
> 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/ <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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