Recently, I have some problems with the crystal water.
1), Should I explicitly include them during minimization or dynamics? And how about the inside water (within the protein) and outside ones?
2),Can I say, oh, cause I added solvent, such as, eps = 80, I should not include the outside water at least?
3), If I do care the few inside water molecules, what is the better eps for the solute(protein+inside water)?
Can anybody show me any general comments?
Thanks in advance!