scaled MD with population based reweighting

Site Authored by William Sinko, PhD

Scaled Molecular Dynamics (scaled MD) with population based reweighting is a molecular simulation method that enhances sampling of long timescaled motions. It was developed in the J. Andrew McCammon Research Group at UC San Diego. Although the method alters the potential energy surface to achieve rapid sampling it relies only on counting the populations of various states to reweight and recover a Boltzmann ensemble of molecular structures. It is particularily useful in protein folding simulations, the construction of free energy surfaces, and biomolecular simulations which aim to generate a large array of molecular conformations for which a relative free energy is desired. Scaled MD with population based reweighting takes advantage of the notion that protein dynamics can be described in a few essential modes or principal components, and that much of the other motions are gaussian and non-essential. For more information please consult the primary publication Pubmed Link . To obtain free python code used for population reweighting please visit the downloads page.

scaled MD was developed by William Sinko, Yinglong Miao, Cesar A.F. de Oliveira, and J. Andrew McCammon