Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations.

ABSTRACT: The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, o

SUBMITTER: Kandel S 

PROVIDER: S-EPMC4733083 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature