[gmx-users] Re: Polarized water model

[David van der Spoel]

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
> file.
There are "extra" parameters in the mdp file that you can use:
userint1
userint2
etc.

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
> "emstep"
> > 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
> positions
> > is performed at each time step?
> If you have shells in your system it is done anyway.
> > 
> > 
> > Xie YH
> 
> 
> 
> 
> _______________________________________________
> 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.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++