Molecular dynamics coupled with a virtual system for effective conformational sampling

J Comput Chem. 2018 Jul 15;39(19):1291-1299. doi: 10.1002/jcc.25196. Epub 2018 Feb 21.


An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc.

Keywords: all-atom model; canonical sampling; enhanced sampling; free-energy landscape; reaction coordinate.

Publication types

  • Research Support, Non-U.S. Gov't