[gmx-users] Polarized water model

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 9 11:35:52 CET 2005

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 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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