Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation.

ABSTRACT: Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of conventional molecular dynamics (cMD) for sampling biomolecular conformations, but they require proper reweighting for free energy calculation. In this work, we systematically compare the accuracy of different reweighting algorithms including the exponential average, Maclaurin series, and cumulant expansion on three model systems: alanine dipeptide, chignolin, and Trp-cage. Exponential average reweighting can recover the original free energy profiles easily only when the distribution of the boost potential is narrow (e.g., the range ≤20k_BT) as found in dihedral-boost aMD simulation of alanine dipeptide. In dual-boost aMD simulations of the studied systems, exponential average generally lead

SUBMITTER: Miao Y 

PROVIDER: S-EPMC4095935 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature