Enhanced solvation force extrapolation for speeding up molecular dynamics simulations of complex biochemical liquids

TL;DR

This paper introduces an advanced solvation force extrapolation method that enhances molecular dynamics simulations of complex biochemical liquids, enabling larger time steps and faster computations without sacrificing accuracy.

Contribution

It presents a novel extrapolation technique combining exponential scaling and dynamic weighting, improving force approximation accuracy and computational efficiency in biomolecular simulations.

Findings

Enhanced extrapolation yields better force accuracy.

Allows larger outer time steps in simulations.

Significantly speeds up molecular dynamics computations.

Abstract

We propose an enhanced approach to the extrapolation of mean potential forces acting on atoms of solute macromolecules due to their interactions with solvent atoms in complex biochemical liquids. It improves and extends previous extrapolation schemes by including additionally new techniques such as an exponential scaling transformation of coordinate space with weights complemented by a dynamically adjusted balancing between the least square minimization of force deviations and the norm of expansion coefficients in the approximation. The expensive mean potential forces are treated in terms of the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model with the Kovalenko-Hirata closure). During the dynamics they are calculated only after every long enough (outer) time interval, i.e., quite rarely to reduce the computational costs. At much shorter (inner) time steps, these forces are extrapolated on the basis of their outer values. The equations of motion are then solved using a multiple time step integration within an optimized isokinetic Nos\'e-Hoover chain thermostat. The new approach is applied to molecular dynamics simulations of various systems consisting of solvated organic and biomolecules of different complexity. Namely, we consider hydrated alanine dipeptide, asphaltene in toluene solvent, miniprotein 1L2Y and protein G in aqueous solution. It is shown that in all these cases, the enhanced extrapolation provides much better accuracy of the solvation force approximation than the existing approaches. As a result, it can be used with much larger outer time steps, leading to a significant speedup of the simulations.