Flexible Gaussian Accelerated Molecular Dynamics to Enhance Biological Sampling.

ABSTRACT: Molecular dynamics simulations often struggle to obtain sufficient sampling to study complex molecular events due to high energy barriers separating the minima of interest. Multiple enhanced sampling techniques have been developed and improved over the years to tackle this issue. Gaussian accelerated molecular dynamics (GaMD) is a recently developed enhanced sampling technique that works by adding a biasing potential, lifting the energy landscape up, and decreasing the height of its barriers. GaMD allows one to increase the sampling of events of interest without the need of a priori knowledge of the system or the relevant coordinates. All required acceleration parameters can be obtained from a previous search run. Upon its development, several improvements for the methodology have been pro

SUBMITTER: Gracia Carmona O 

PROVIDER: S-EPMC10536968 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature