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

[Mikhail Stukan]

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?

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