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

[Peter Hamm]

Thanks,  Justin, for the quick response. Yes, I can see what to change 
in gmxlib/bondfree.c

Best wishes

Peter
>
>
> 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
>