[gmx-users] Re: Polarizable halide (Iodide)
David van der Spoel
spoel at xray.bmc.uu.se
Wed Mar 2 11:06:12 CET 2011
On 2011-03-02 09.44, Mikhail Stukan wrote:
> 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:
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
> Many thanks in advance,
> 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
>> 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
>> Your help will be greatly appreciated
>> ~ 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
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