David van der Spoel
spoel at xray.bmc.uu.se
Wed Feb 24 14:46:17 CET 2010
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  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 :).
> 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
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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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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