simtk.org

Hi all,
I have a pre-equilibrated cell, to which I added a ligand that dips over the edge of the cell, forming bad contacts with water.

minimizeEnergy() is unable to remove the contacts - does this function work across the boundary? It can be fixed by increasing the z direction of the PBC (and recovering with a barostat if necessary), just wondering how it works.

If your initial conformation is too bad, the minimizer won't be able to fix it. Minimization is for making small changes to the atom positions. If you have two molecules right on top of each other, it's unlikely to be able to fix that. In this case, your initial energy is over 2 trillion kJ/mol, which is way beyond what you can reasonably expect it to fix.

You need to identify which water molecules the ligand is clashing with and remove them. Once that's done, things should work a lot better.