[gmx-users] Polarizative models for water

David van der Spoel spoel at xray.bmc.uu.se
Mon Apr 28 10:49:38 CEST 2008

Dmitri Dubov wrote:
> (for David van der Spoel, imho)
> Dear David,
> I am doing some similations of large water cluster with tip4p flexible model. I would like to include polarizability effect in the simulation, but trying it get twofold problem.
> First, I need the input gro-file with dummy and shell particles. I failed to apply your utility "mkyaw" to my tip4p-structure file directly, since it remained in final file virtual sites MW. Then I reduced my tip4 structure to spc and generated correct gro-file with dummy and shell and without virtuals MW. But! I see that coordinates of both dummy and shell particles coincide with oxygen atoms! Is it acceptable or the result of some mistake of mine?
> I cannot examine this (and it is the second problem), since I don't understand how topology file should be generated. I find here the instruction "to use sw.itp instead of spc.itp". But formal replacement in pdb2gmx option "-water" is impossible. Should I
> #include "sw.itp"
> into top-file manually? Is it enough? Could you give me more detailed instructions?
> And the last question. As I know at least three polarizative models of water are implemented in GMX. The sw.itp file with your parametrization is in GROMACS distributives, the file of parameters for Roux group's model can be found in gmx-users archive. What about the third model (I mean the model of Gunsteren group)? Is it possible to get their parameter file?

You can easily make it yourself. Read chapter 5 in the manual and read 
the paper carefully.

For mkyaw you should check the extra flags (mkyaw -h).

You don't need pdb2gmx anywhere for water clusters.

> Thank you in advance
> Sincerely,
> Dmitri
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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