Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations.

ABSTRACT: Accelerated molecular dynamics (aMD) has been shown to enhance conformational space sampling relative to classical molecular dynamics; however, the exponential reweighting of aMD trajectories, which is necessary for the calculation of free energies relating to the classical system, is oftentimes problematic, especially for systems larger than small poly peptides. Here, we propose a method of accelerating only the degrees of freedom most pertinent to sampling, thereby reducing the total acceleration added to the system and improving the convergence of calculated ensemble averages, which we term selective aMD. Its application is highlighted in two biomolecular cases. First, the model system alanine dipeptide is simulated with classical MD, all-dihedral aMD, and selective aMD, and these resul

SUBMITTER: Wereszczynski J 

PROVIDER: S-EPMC2976571 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature