[gmx-users] Solvent

[David van der Spoel]

On Thu, 2003-02-20 at 16:28, Dmytro wrote:
> Hi,
> 
> I'm prepearing the system for simulation. After genbox I'm doing md with 
> posres of protein atoms. From the very begining  solvent rapidly 
> desrease its own volume and becomes more dence. In my box holes start to 
> appear ! Genbox generated solvent molecules with default  pressure. 
> I'didn't used pressure coupling in the posres. What it coulbd be related 
> for?

What's the density? If it is too low density solvent will cluster
together. You have to do p coupling to get the right density.
> 
> Yours,
> Dmitry
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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