[gmx-users] Thermodynamic State of SPC/E bulk water, by genbox

[David van der Spoel]

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.

> thanks
> sikandar
>
> 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:
>
>         Hi
>
>         When a bulk SPC/E water box(.gro) is created using the command
>         "genbox
>         -cs spc216.gro -box 4.0 4.0 4.0", what is the thermodynamic
>         condition of
>         water?
>
>         Is it 300K at 1atm?
>
>         thanks
>         sikandar
>
>     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