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. Sander On Feb 24, 2010, at 13:23 , 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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > 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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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