A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method.

ABSTRACT: There has been a resurgence of interest in free energy methods motivated by the performance enhancements offered by molecular dynamics (MD) software written for specialized hardware, such as graphics processing units (GPUs). In this work, we exploit the properties of a parameter-interpolated thermodynamic integration (PI-TI) method to connect states by their molecular mechanical (MM) parameter values. This pathway is shown to be better behaved for Mg²⁺ → Ca²⁺ transformations than traditional linear alchemical pathways (with and without soft-core potentials). The PI-TI method has the practical advantage that no modification of the MD code is required to propagate the dynamics, and unlike with linear alchemical mixing, only one electrostatic evaluation is needed (e.g.,

SUBMITTER: Giese TJ 

PROVIDER: S-EPMC5849537 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature