[gmx-users] swm4-ndp water with anisotropic polarizibility

[Justin Lemkul]

On 3/11/14, 7:27 AM, Peter Hamm wrote:
> Hi
>
> I'm trying to set up a slightly modified version of swm4-ndp water with
> anisotropic polarizibility. In contrast to sw-water, where the Drude (shell)
> particle is connected to  a dummy particle, it is connected to the oxygen in
> swm4-ndp. In sw.itp, ananisotropic polarizibility is defined by:
>
> [ water_polarization ]
> ; See notes above. Alphas in nm^3 (See ref. above)
> ; O H H D S funct  al_x  al_y     al_z          rOH     rHH     rOD
>    1 2 3 4 5 1   0.001415 0.001528 0.001468      0.09572 0.15139 0.0137408
>
> I guess, the "4 5" means that the Drude particle (5) is connected to the dummy
> particle  (4). I therefore changed it to
>
> [ water_polarization ]
> O H H D S funct  al_x      al_y      al_z             rOH rHH     rOD
> 1 2 3 1 5 1      0.0010583 0.0011435 0.0010975       0.09572 0.15139 0.0257788
>
> so that Drude particle (5) is now connected to the oxygen (1). This however
> generates a warning in grompp:
>
> "WARNING 1 [file swm4-ndp-mod.top, line 33]: Duplicate atom index (1) in
> water_polarization"
>

You've repeated atom number 1, which the code is interpreting as both a Drude 
and the oxygen atom.

> My question: Is [ water_polarization ] specific for sw-water with the shell
> particle necessarily connected to the dummy particle, or, can I ignore the
> warning, or, is there another syntax to do what I want to do (i couldn't find
> any real description of the syntax of [ water_polarization ]).
>
> Best wishes, and thanks in advance for any help you can offer
>

The topology format and the code itself for water polarization is specific to 
the setup of the SW model.  I have been working on generalizing the shell/Drude 
code for a while now, and the introduction of general anisotropy is not 
difficult to do, though my implementation is largely untested and therefore not 
suitable for the public just yet.  The code in gmxlib/bondfree.c (water_pol 
function) can be easily modified.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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