[gmx-users] Re: Polarized water model

xieyh at hkusua.hku.hk xieyh at hkusua.hku.hk
Fri Mar 11 11:11:41 CET 2005

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

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?

3. In your shell model, dummy atoms are used. However, can I directly connect
the shell particle to oxygen atoms without using dummy atoms?

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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