[gmx-users] Re: Polarized water model

xieyh at hkusua.hku.hk xieyh at hkusua.hku.hk
Wed Mar 9 15:37:27 CET 2005

Dear David:

Thanks. In addition, can you tell me the normal values of "emtol" and "emstep"
for such shell MD? 

By the way, how to realize that the minimization of the shell particle positions
is performed at each time step?

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
> 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
> 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.


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