From: Steven Cohen (
Date: Thu Oct 06 2016 - 14:52:05 CDT

I'm running MDFF to fit a .pdb into my EM density map and have noticed that
my simulations are running to near (~90%) convergence before cutting out
due to exceeding the per-atom velocity. To the best of my knowledge, this
seems to occur as the structure is getting pulled into the core of the EM
density. Is there a good way to stop the program from cutting out so that I
can reach a final structure?

Steven Cohen
Graduate Student, Drennan Lab
Department of Chemistry
Massachusetts Institute of Technology