[gmx-users] Re: Polarized water model
David van der Spoel
spoel at xray.bmc.uu.se
Fri Mar 11 11:53:51 CET 2005
On Fri, 2005-03-11 at 18:11 +0800, xieyh at hkusua.hku.hk wrote:
> Dear David:
> Thanks. I have tried many times as you said. There are still three problems to
> get your help.
> 1. In shell model, as mentioned in your paper, shell particle position was
> performed at each time step. But it is very time-consuming. If I wanna make
> this minimization at every 5th step. How should I input this parameter in mdp
There are "extra" parameters in the mdp file that you can use:
Then you have to do the programming logic in relax_sh.c
> 2. If I solvate protein in such shell water, in the step of PR, why EM can not
> always converge? (even emtol=0.1, run in doule precision). Any suggestion?
No. Force field incompatibility.
> 3. In your shell model, dummy atoms are used. However, can I directly connect
> the shell particle to oxygen atoms without using dummy atoms?
It would be a different model, and we have tried such models. They were
not as good as the published SW models.
> Thanks very much.
> Xie YH
> Hong Kong Univ.
> On Wed, 2005-03-09 at 22:37 +0800, xieyh at hkusua.hku.hk wrote:
> > Dear David:
> > Thanks. In addition, can you tell me the normal values of "emtol" and
> > for such shell MD?
> emtol = 0.1 kJ/mol
> emstep doesn't matter (if I'm not terribly wrong)...
> > By the way, how to realize that the minimization of the shell particle
> > is performed at each time step?
> If you have shells in your system it is done anyway.
> > Xie YH
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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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