[gmx-users] Creating a simple water box

[Dallas Warren]

Is the "close contact" really an issue? As soon as you start any sort of MD
that will quickly adjust itself.

On Sat, 14 Mar. 2020, 7:23 pm dodia, <dodia at mpip-mainz.mpg.de> wrote:

> 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
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