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

Sikandar Mashayak symashayak at gmail.com
Fri Jun 18 20:22:06 CEST 2010

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.


On Fri, Jun 18, 2010 at 12:20 PM, David van der Spoel
<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.
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