This was my personal git repository for the mdff plugin of VMD while I worked for the Theoretical and Computational Biophysics Group at the University of Illinois Urbana-Champaign. The molecular dynamics flexible fitting (MDFF) method can be used to flexibly fit atomic structures into density maps (usually Cryo-EM, or low-resolution X-ray crystallography for xMDFF). The method consists of adding external forces proportional to the gradient of the density map into a molecular dynamics (MD) simulation of the atomic structure.

I no longer work at UIUC or with current mdff development, so this repo is now archived. For current MDFF information please see the official site