[gmx-users] water density

Erik Lindahl lindahl at csb.stanford.edu
Tue May 11 19:30:58 CEST 2004


First, when the box volume decreases the density will increase and vice 
versa - there's a strict inverse proportionality between them :-)

 From your description it sounds as if you turned on pressure scaling 
for a system that wasn't equilibrated. In that case, the temporary high 
forces this might lead to a rapid volume expansion.

If you try to simulate water in a box that is too large you'll get 
clusters. Compare with a glass of water in a space shuttle - the water 
won't expand to fill the entire shuttle at low density, but will form a 
sphere in vacuum.



On May 11, 2004, at 8:12 PM, Linda wrote:

> Hi, all,
> 	Before gmx-users have disscussed water density to run MD. As David 
> suggested, we can delete some numbers of water to adjust water 
> density. I follow this idea, but when I equilibate system with NPT 
> ensemble, I found the box size was decreased, and the water density 
> decreases. I think the reason is the pressure adjust the density. when 
> I equilibate system with NVT, the water distribution is not 
> equal.There is no water in some space of simulation box.
> Does anyone (David?) have experience on water density? Thanks!
> Linda
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