[gmx-users] water density
spoel at xray.bmc.uu.se
Tue May 11 22:45:08 CEST 2004
On Tue, 2004-05-11 at 20:12, 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!
if you have too few waters and simulate NVT you'll get a bubble of
vacuum. If you have even fewer waters you get clusters. If box size is
decreased density increases (in contrast to what you write)
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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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