Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units.

ABSTRACT: Molecular dynamics (MD) simulations of proteins are commonly used to sample from the Boltzmann distribution of conformational states, with wide-ranging applications spanning chemistry, biophysics, and drug discovery. However, MD can be inefficient at equilibrating water occupancy for buried cavities in proteins that are inaccessible to the surrounding solvent. Indeed, the time needed for water molecules to equilibrate between the bulk solvent and the binding site can be well beyond what is practical with standard MD, which typically ranges from hundreds of nanoseconds to a few microseconds. We recently introduced a hybrid Monte Carlo/MD (MC/MD) method, which speeds up the equilibration of water between buried cavities and the surrounding solvent, while sampling from the thermodynamically c

SUBMITTER: Ben-Shalom IY 

PROVIDER: S-EPMC8716912 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature