[gmx-users] Polarizable halide (Iodide)

[aldi asmadi]

Hi David,

On Wed, Mar 2, 2011 at 12:12 AM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> 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."
Does this also include the implementation of thole polarization in
shell polarizable model for long chain hydrocarbons?

>
>>
>> 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
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