pronk at cbr.su.se
Wed Feb 24 14:00:48 CET 2010
You got pretty close to what the density of SPC water is at 298K
According to "Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking temperatures of maximum density", William L. Jorgensen, Corky Jenson, J. Comp. Chem, Volume 19 Issue 10, Pages 1179 - 1186 (1998)
it should be 0.985g/ml, and TIP4P will give you 1.001g/ml.
Remember that you're simulating SPC water, not real water.
On Feb 24, 2010, at 13:23 , Sunil Thapa wrote:
> Respectable Experts
> 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users