[gmx-users] density

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 24 13:51:25 CET 2010

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)?

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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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