Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations.

ABSTRACT: Adequate sampling of conformation space remains challenging in atomistic simulations, especially if the solvent is treated explicitly. Implicit-solvent simulations can speed up conformational sampling significantly. We compare the speed of conformational sampling between two commonly used methods of each class: the explicit-solvent particle mesh Ewald (PME) with TIP3P water model and a popular generalized Born (GB) implicit-solvent model, as implemented in the AMBER package. We systematically investigate small (dihedral angle flips in a protein), large (nucleosome tail collapse and DNA unwrapping), and mixed (folding of a miniprotein) conformational changes, with nominal simulation times ranging from nanoseconds to microseconds depending on system size. The speedups in conformational sampl

SUBMITTER: Anandakrishnan R 

PROVIDER: S-EPMC4375717 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature