Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer

GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models

GENeralized-Ensemble SImulation System (GENESIS) is a molecular dynamics (MD) software developed to simulate the conformational dynamics of a single biomolecule, as well as molecular interactions in large biomolecular assemblies and between multiple biomolecules in cellular environments. To achieve the latter purpose, the earlier versions of GENESIS emphasized high performance in atomistic MD simulations on massively parallel supercomputers, with or without graphics processing units (GPUs). Here, we implemented multiscale MD simulations that include atomistic, coarse-grained, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. They demonstrate high performance and are integrated with enhanced conformational sampling algorithms and free-energy calculations without using external programs except for the QM programs. In this article, we review new functions, molecular models, and other essential features in GENESIS version 2.1 and discuss ongoing developments for future releases.

Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering

Buried ionizable groups in proteins often play important structural and functional roles. However, it is generally challenging to study the detailed molecular mechanisms solely based on experimental measurements. Free energy calculations using atomistic simulations, on the other hand, complement experimental studies and can provide high temporal and spatial resolution information that can lead to mechanistic insights. Nevertheless, it is also well recognized that sufficient sampling of such atomistic simulations can be challenging, considering that structural changes related to the buried charges may be very slow. In the present study, we describe a simple but effective enhanced sampling technique called replica exchange with charge tempering (REChgT) with a novel free energy method, multisite λ dynamics (MSλD), to study two systems containing buried charges, pKa prediction of a small molecule, orotate, in complex with the dihydroorotate dehydrogenase, and relative stability of a Glu-Lys pair buried in the hydrophobic core of two variants of Staphylococcal nuclease. Compared to the original MSλD simulations, the usage of REChgT dramatically increases sampling in both conformational and alchemical spaces, which directly translates into a significant reduction of wall time to converge the free energy calculations. This study highlights the importance of sufficient sampling toward developing improved free energy methods.