[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
> 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