[gmx-users] Dodecahedron Box size and Appropriate number of SOL molecules

[Apramita Chand]

Hey,
 Thanks a lot Tsjerk for your advice regarding box size. You've mentioned
that we could take a box size which lets us add a bit more water than
needed and we could delete some molecules. So can I use genbox to add water
and then delete any number of water molecules to reach my target solvent
number? I'm using a box size of say 2.9 and I want a box of peptide,5 urea
and 494 water molecules. genbox adds 566 water molecules. Do I have to
simply delete the extra water molecules and that would be okay after
equilibration?
So there is basically no restriction that only a fixed  number of water
molecules  should be present in a particular box,right?


Regards,
Apramita Chand