On 2/24/10 1:23 PM, Sunil Thapa wrote:
Respectable Experts
Grettings
I am studying diffusion of an oxygen molecule in 255 molecule of SPC
water. I need to determine diffusion coefficient at temperature 298 K
and 1 atm pressure. In order to do that
using editconf I scaled the density of the system including oxygen to
1g/l. I checked the density after energy minimization (steepest descent)
which gave the reading of 0.76 g/l. After that I equilibrated the system
to pressure of 1 bar and temperature of 298 K using NPT simulation
(berendsen). The density reading was 0.98. When I checked the density
table at 298 K, it was about 0.9927 g/l.
I am afraid if my density is not consistent with experimental density of
the system. Is this some bug of gromacs 3.2.1 or my understanding of
thermodynamics is very poor for pressure and liquid density. Please help
me on this.
Should I use the same NPT simulation to derive the experimental
diffusion coefficient ?
Looking forward to hearing from you
Neal, Nepal
It depends on the water model and your settings. Did you use PME and
long-range corrections for LJ (Dispcorr = EnerPres)?
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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