[gmx-users] Re: Polarized water model

[David]

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
> 
> 
> 
> 
> 
> On Wed, 2005-03-09 at 18:10 +0800, xieyh at hkusua.hku.hk wrote:
> > Dear users:
> > 
> > I would like to use polarized water model (shell MD) in my simulations of
> > protein solvated in SW water.
> 
> This may work, but because the force fields are not tested together it
> will probably give ill-defined results, in particular because of
> combination rules for generating water-protein interactions.
> 
> > 
> > According to the instruction in the mailing list. I go on as the follows.
> > 
> > 1. Using "mkyaw" program to transform "spc216.gro" box to "sw216.gro", as
> well
> > as using "sw.itp" instead of "spc.itp". 
> > 
> > But has this SW model been already energy minimized? Or, I need a separate
> > energy minization before I add my protein into this solvent?
> If you want to do anything, start by running a short simulation of SW
> without anything in there.
> 
> > 
> > 2. When energy minimization, as mentioned in GMX manual, emtol should be 1
> > KJ/(mol.nm) in the case of shell MD, is it possible? Even I have only SW
> water
> > in my system, such small value is hard to obtain. If I set e.g. emtol = 1000,
> > the errors in PR step will be emerged (as the following). Can anybody tell me
> > how to deal with such problem? 
> > 
> > 3. Also, does EM for shell MD run in double precision? If yes, how to realize
> > it?
> You have to run everything in DP.
> > 
> 
-- 
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
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