On 2/24/10 2:00 PM, Sander Pronk wrote:
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.
Correct, but note that
1. Jorgensen uses a funky switch function rather than PME (undocumented,
except in my paper JCTC 2 [2006] p. 1)
2. Monte Carlo iso MD (although that shouldn't make a difference)
3. Long range corrections to the energy, but not to the pressure
in case you want to reproduce his results :).
Cheers, David,
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
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