Okay, thanks for the PBC advise. But the question I was wondering was the water molecule concentration within the box. I mean, should I just generate a PDB file with random coordinates for minimum number of TIP3 molecules, and then use CHARMM to strip out the overlapping waters? And how can I predict the minimum number of water molecules, given that I know the dimensions of the protein?
And in general, how do you usually prepare the explicit water? Is there an easier way than to read a randomly generated PDB file, like: generate 9999 TIP3P molecules and setup their coordinates randomly in CHARMM?