[gmx-users] David, still polarization!

David van der Spoel spoel at xray.bmc.uu.se
Mon Mar 14 10:57:13 CET 2005

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.
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
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

More information about the gromacs.org_gmx-users mailing list