[gmx-users] Thermodynamic State of SPC/E bulk water, by genbox
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jun 18 20:34:50 CEST 2010
On 2010-06-18 20.22, Sikandar Mashayak wrote:
> I am concerned about the number density of water. At T = 300 K and P = 1
> atm, SPC/E water has certain number density (no. of molecules/nm^3).
> With genbox I get .gro file with 34.04 molecules/nm^3 number density,
> which will remain constant even if I do equilibration in NVT simulation
> set up. So does that 34.04 molecules/nm^3 corresponds to thermodynamic
> condition of water at 300K and 1 atm.
If you want to do NVT production, you still need to do an NPT
equilbration, and extract the average density, otherwise your pressure
will not be 1 atm in NVT.
> On Fri, Jun 18, 2010 at 12:20 PM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
> On 2010-06-18 18.24, Sikandar Mashayak wrote:
> When a bulk SPC/E water box(.gro) is created using the command
> -cs spc216.gro -box 4.0 4.0 4.0", what is the thermodynamic
> condition of
> Is it 300K at 1atm?
> No. You have to equilibrate because the box is not completely full.
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
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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.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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