[gmx-users] H2O water density = 6.4617 g/l << 1000 g/l

[Mark Abraham]

Chih-Ying Lin wrote:
> Hi
> I am creating the water box with the following command.
> The maxsol = 800; but # of SOL = 27;
> The H2O  water density =  6.4617 g/l  << 1000 g/l
> 
> Did I do anything wrong on my genbox command or 1w.gro file?
> 
> Thank you
> Lin
> 
> 
> genbox -cp 1w.gro -cs 1w.gro -o box.gro -box 5 5 5 -maxsol 800
> 
> Output configuration contains 81 atoms in 27 residues
> Volume                 :         125 (nm^3)
> Density                :      6.4617 (g/l)
> Number of SOL molecules:     27
> 
> 
> 
> Here is the  1w.gro
> 
> 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
>     3
>     1SOL     OW    1    .230    .628    .113
>     1SOL    HW1    2    .137    .626    .150
>     1SOL    HW2    3    .231    .589    .021
>    1.86206   1.86206   1.86206

So when you tile these cubes of side length 1.86nm in a 3x3x3 grid, you 
over-fill a cube of side length 5nm and get 27 water molecules. Use the 
standard water .gro files in the distribution and then minimize and 
equilibrate.

Mark