Re: SWM4-NDP PSF File

From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu Sep 27 2018 - 08:41:10 CDT

Hi Julian,

Without looking back at the code, I don't have an answer which speaks
directly to your inquiry. However, I will say that all water models in NAMD
(including lone pair models) have specialized routines that often ignore
some or all of the LPHOST section of the PSF. Thus, while I suspect there
is a logical explanation for that format, it's also possible that it will
not exactly match the NAMD internals,which instead use heuristics based on
atom masses, etc.

HTH,
BKR

On Thu, Sep 27, 2018, 3:49 AM Julian Müller <mueller_at_pctc.uni-kiel.de>
wrote:

> Hello,
>
> i am trying to set up different solvent boxes using the drude
> polarizable SWM4-NDP water model. I downloaded the example files for 216
> SWM4-NDP water from https://www.ks.uiuc.edu/Research/Drude. I am a
> little puzzled by the !NUMLP NUMLPH section, especially the exact
> meaning of the second entry in the following lines:
>
> 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
>
> Searching available documentation it seems this number identifies the
> host atom the lone pair is attached to. Therefore i would intuitively
> expect the numbers to be 1, 6, 11 (i.e. the atom IDs of the Oxygen
> atoms) and ascending from there up to the total number of atoms in the
> system, since the number of atoms per SWM4-NDP water is 5 including the
> drude particle. Is there a reason that this number is incremented by 4
> per lone pair and not by 5? Am i interpreting the line incorrectly or is
> there maybe an error with this .psf file due to the conversion from a
> four atom TIP4P model? Any help here would be greatly appreciated.
>
> best regards
>
> Julian Müller
>
> --
> Dr. Julian Müller
> Institute for Physical Chemistry
> Christian-Albrechts-Universität zu Kiel
> Max-Eyth Strasse 2
> 24118 Kiel
>
> phone: 0049 431 880-5820
> e-mail: mueller_at_pctc.uni-kiel.de
>
>

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