[gmx-users] Creating a simple water box

[dodia]

Dear gromacs users,

I was trying a simple gmx solvate test on a water box of size 25*20*20 
angstrom, creating a water box of density 1 g/cm^3. By my calculations 
the no. of water molecules in the box should by 332 (each water molecule 
has a volume of (3.11 angstrom)^3). When I use the solvate command:

gmx solvate -cs spc216 -box 2.5 2 2 -o test2.pdb -maxsol 332

with gromacs 5.0.7, I get 291 water molecules in the box, and the 
density as 0.87 g/cm^3

with gromacs 2016.1, I get 295 water molecules in the box, and the 
density as 0.88 g/cm^3

When I try using the -scale option:

gmx solvate -cs spc216 -scale 0.40 -box 2.5 2 2 -o test.pdb -maxsol 332

I can get a density of 0.993 g/cm3, however when I visualize the 
structure, I can notice a lot of close contact between O-O atoms (the 
distance between O-O atoms becomes lower than 1.49 angstroms, the O-O 
bond length). So is there any other way to fine tune the gmx solvate 
command so as to generate the water box with density close to 1 g/cm^3, 
without the close contact problem?

Best Regards,
Mayank Dodia