[gmx-users] Polarized water model

[David van der Spoel]

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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++