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Wed Feb 24 14:58:48 CET 2010
> Date: Wed, 24 Feb 2010 14:46:17 +0100
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] density
> 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)
Well, this does make a difference if some interactions are not switched.
MC will see the jump in the potential at the cut-off, whereas MD which
samples according to the forces does not.
> 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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> 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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