CECAM tutorial: Atomistic Monte Carlo Simulations of Bio-molecular Systems

Atomistic Markov Chain Monte Carlo simulations (MC) offer an interesting and complementary approach to Molecular Dynamics (MD) in the study of long time scale biophysical phenomena. MC simulations follow well established techniques to obtain a statistical physics description of a system using the potential energy function, but without solving the equations of motion. While a temporal description of the simulated process is sacrificed, questions about probabilities, temperature dependence, effects of prevailing conditions etc. can often be answered at a minuscule fraction of the computing cost (and hence also the energy cost and carbon footprint) of an adequately long MD simulation. We have previously used replica exchange MC simulations to describe the folding of a complex 92 residue alpha + beta protein with an experimental folding time of about one second. We have also applied MC techniques to study intrinsically disordered proteins, peptide aggregation and the influence of macro-molecular crowding on protein behaviour. We believe that MC techniques are severely underused in biophysical research, owing to the dearth of exposure to the technique in contrast to MD within the community. Our tutorial is an effort to introduce researchers in the field to MC techniques in sufficient detail for them to use it in their own research.

This CECAM Tutorial is organized by Sandipan Mohanty, Olav Zimmermann, and Jan Meinke (Jülich Supercomputing Centre) and will take place at Forschungszentrum Jülich, Jülich Supercomputing Centre.