[gmx-users] Polarizable halide (Iodide)
Abhijeet Joshi
abhijoshi129 at gmail.com
Tue Mar 1 23:10:59 CET 2011
Oh ohk,
I have been running in parallel
Thanks David,
On Tue, Mar 1, 2011 at 3:12 PM, 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.
>
>
>
>> 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
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Abhijeet Joshi
Research Assistant
Molecular Thermodynamics and Statistical Mechanics Research Group
University of Wisconsin-Madison
http://www.engr.wisc.edu/groups/mtsm/index.shtml
aajoshi2 at wisc.edu
608-320-9215
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110301/043df0c3/attachment.html>
More information about the gromacs.org_gmx-users
mailing list