Accelerating Replica Exchange Molecular Dynamics: A Comparison of Hydrogen Mass Repartitioning and Light Water Models.

ABSTRACT: Accelerating conformational sampling through changes in molecular mass is an attractive option in biomolecular modeling. Here, we examine the utility and compare the efficiency of hydrogen mass repartitioning (HMR) and light water (LW) models in the context of replica exchange (RE) simulations of an alanine dipeptide. To maintain integrator stability, we introduced scaling of integration steps with RE temperatures and determined their maximum values, assuring the stability of RE simulations. HMR2 and HMR3 models featuring doubled and tripled hydrogen masses and, to a lesser extent, the LW model reproduce the energetic and conformational properties of alanine dipeptide in water compared to the HMR1 reference. This conclusion is based on comparing kinetic and potential energies, free energy

SUBMITTER: Bowers SR 

PROVIDER: S-EPMC12854735 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature