[gmx-users] David, still polarization!

[David van der Spoel]

On Mon, 2005-03-14 at 17:54 +0800, xieyh at hkusua.hku.hk wrote:
> Dear David:
> 
> Thanks for your precious suggestion. However, I can not still get a smooth
> simulation on the topics of non-polarized protein solvated in the polarized
> shell water model, no matter how I adjust those input parameters.
> 
> As I think, it is almost impossible to simulate a non-polar protein in the
> polarized water solvent via GMX. 
This is probably correct, unless you define all the nonbonded
interactions between protein and solvent in the topology. But you have
to generate parameters.

> 
> On the contrary, assuming I have a polarized protein molecule, is it possible to
> simulate it in the original SPC solvent?
You have to create a force field for it.

> 
> Thanks again.
> 
> 
> 
> Xie YH
> Hong Kong Univ.
> 
> 
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-- 
David.
________________________________________________________________________
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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