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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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