On 2011-03-01 22.47, aldi asmadi wrote:
Hi David,
On Wed, Mar 2, 2011 at 12:12 AM, David van der Spoel
<[email protected]> 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.
[email protected] 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.
[email protected] http://folding.bmc.uu.se
--
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