[gmx-users] Polarizable halide (Iodide)

[David van der Spoel]

On 2011-03-01 22.47, aldi asmadi wrote:
> 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?
Don't know. Try it.

>
>>
>>>
>>> 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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-- 
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