[gmx-users] polarizable water

David spoel at xray.bmc.uu.se
Tue Nov 22 18:40:25 CET 2005

On Tue, 2005-11-22 at 17:34 +0000, Michael Bajomo wrote:
> Dear guys,
> I am interested in simulating small peptides in polarizable water, I
> know this is possible in Gromacs (using the Shell model) but I don't
> know exactly how to do it. I am new to gromacs, please accommodate my
> ignorance. 
In fact this is not trivial since the force fields have not been
developed together and hence e.g. HBond lengths might be weird. You will
also have to modify force field files manually.

If you still want to pursue this, please start by making a topology for
the peptide in regular water, and then carefully merge a pol. water
topology in the peptide topology.

Before you start I'd advise you to read some recent papers from the
group of Benoit Roux.
> Thank you for your quick and helpful reply
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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