A Sinking Approach to Explore Arbitrary Areas in Free Energy Landscapes.

ABSTRACT: To address the time-scale limitations in molecular dynamics (MD) simulations, numerous enhanced sampling methods have been developed to expedite the exploration of complex free energy landscapes. A commonly employed approach accelerates the sampling of degrees of freedom associated with predefined collective variables (CVs), which typically tend to traverse the entire CV range. However, in many scenarios, the focus of interest is on specific regions within the CV space. In this paper, we introduce a novel "sinking" approach that enables enhanced sampling of arbitrary areas within the CV space. This method, referred to as SinkMeta, "sinks" the interior bias potential to create a restraining potential "cliff" at the grid edges, thus confining the exploration of CVs in MD simulations to a pre

SUBMITTER: Pan Z 

PROVIDER: S-EPMC12188410 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature