On 2011-03-02 09.44, Mikhail Stukan wrote:
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?
I have an open issue on this:
http://redmine.gromacs.org/issues/713
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
forum.
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.
sp...@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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
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