Population based reweighting of scaled molecular dynamics.

ABSTRACT: Molecular dynamics simulation using enhanced sampling methods is one of the powerful computational tools used to explore protein conformations and free energy landscapes. Enhanced sampling methods often employ either an increase in temperature or a flattening of the potential energy surface to rapidly sample phase space, and a corresponding reweighting algorithm is used to recover the Boltzmann statistics. However, potential energies of complex biomolecules usually involve large fluctuations on a magnitude of hundreds of kcal/mol despite minimal structural changes during simulation. This leads to noisy reweighting statistics and complicates the obtainment of accurate final results. To overcome this common issue in enhanced conformational sampling, we propose a scaled molecular dynamics met

SUBMITTER: Sinko W 

PROVIDER: S-EPMC3808002 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature