AMBER Free Energy Tools: A New Framework for the Design of Optimized Alchemical Transformation Pathways.

ABSTRACT: We develop a framework for the design of optimized alchemical transformation pathways in free energy simulations using nonlinear mixing and a new functional form for so-called "softcore" potentials. We describe the implementation and testing of this framework in the GPU-accelerated AMBER software suite. The new optimized alchemical transformation pathways integrate a number of important features, including (1) the use of smoothstep functions to stabilize behavior near the transformation end points, (2) consistent power scaling of Coulomb and Lennard-Jones (LJ) interactions with unitless control parameters to maintain balance of electrostatic attractions and exchange repulsions, (3) pairwise form based on the LJ contact radius for the effective interaction distance with separation-shifted s

SUBMITTER: Tsai HC 

PROVIDER: S-EPMC10329732 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature