[gmx-users] Re: Polarizable halide (Iodide)

[David van der Spoel]

On 2011-03-02 09.44, Mikhail Stukan wrote:
> David,
>
> What should not be working in the current version?
> Do you mean that any polarizable model (water for example) can run on a single processor only?
> I am currently using the model by Roux et al. for NaCl solution in SWM4-NDP model and everything seems to be working fine.
> I also had some problems with the collapsing of the system which seems to be solved by setting explicitly all pair interactions in [nonbond_param] statement (I had a feeling that mixing rule did not work for some reason). The results are very reasonable.
> Does it mean that I am doing something completely wrong?
>
I have an open issue on this:

http://redmine.gromacs.org/issues/713

maybe you can download the test files (based on the same model) that I 
put there and check them. Let's continue the discussion in the redmine 
forum.

> Many thanks in advance,
> Mikhail
>
>
> On 2011-03-01 22.06, Abhijeet Joshi wrote:
>> Hi all,
>>
>>              I am trying implement polarizable model for halides
>> suggested by Roux group.
>> I am not able to equilibrate such system.
>
> In present gromacs versions this runs on 1 processor (core) only.
>
>>
>> System: Sodium Iodide in water
>> I am using following topology file for iodide.
>>
>> Anybody has any clue what might be happening?
>>
>> Question 2: I am having trouble finding implementation details for
>> thole_polarization.
>> How would that appear in topology file?
>>
>>
>>
>> ;
>> ; Topology file for iodide polarizable
>>
>> [ moleculetype ]
>> ; molname    nrexcl
>> I        1
>>
>> [ atoms ]
>> ; id    at type    res nr     residu name    at name        cg nr    charge
>> 1       II             1              SI        CI1        1       3.733085
>> 2       IS            1              SI        SI        1        -4.733085
>>
>>
>> [ polarization ]
>> ; See notes above.    alpha (nm^3)
>> 1    2    1     0.007439
>>
>>
>>
>> [ exclusions ]
>> ; iatom excluded from interaction with i
>> 1    2
>> 2    1
>>
>> #ifdef POSRES
>> ; Restrain the oxygen...
>> [ position_restraints ]
>> ; iatom type    fx    fy    fz
>> 1    1    100    100    100
>> #endif
>>
>>
>>
>> Your help will be greatly appreciated
>>
>> Thanks
>> ~ Abhijeet
>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell&  Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se