I wish to insert an specific number of water molecules in a pbc box with the solute centered in the box. Is there any systematic way of doing this? I have used solvate with the -maxsol keyword to specify the number of water molecules. My concern is that my default pbc box can accommodate to a maximum of 800 water molecules, so if I insert less water molecules, would it be a problem with this?
Another way to ask this question is: how can I create a pbc box with a solute centered and add an specific number of molecules solvent systematically?
Yes, either your box will compress (when a barostat is applied under an NPT ensemble), or you will develop voids (bubbles) in the simulation box if you are simulating under an NVT ensemble, which will then lead to surface-tension effects around those voids.
You can’t. Those are the two inevitable outcomes under those two ensembles. The question is, why do you need to restrict the number of waters in your unit cell to some value that does not completely fill the volume?
This is not the way to do that. The best way to save on computational time is to use a non-cubic box for your solute, e.g. rhombic dodecahedron or truncated octahedron. You’ll save something like 23% of the volume for the same periodic distance. If you just use fewer waters, you’ll have problems like I mentioned, and if you’re running NPT simulations, the box will compress down some and you may violate the minimum image convention, rendering your “fast” simulations very wrong.
Thanks for your useful comment. I have the same problem and I want to fill the box with water to get to a specific concentration (with my polymer chains), but when I enlarge the simulation box (to have a appropriate pbc), I have to add more water molecules. would you please tell me what can I do with this problem?