Accelerating Variable Cell Shape Molecular Dynamics with a Position-Dependent Mass Matrix
Martin Sommer-Jörgensen, Marco Krummenacher, Stefan Goedecker
TL;DR
This paper introduces a new method in molecular dynamics simulations that increases time steps by using a position-dependent mass matrix, allowing faster and more efficient simulations.
Contribution
The novel contribution is adapting MTMD with a position-dependent mass matrix for variable cell shape systems and demonstrating its efficiency.
Findings
The method increased the time step by a factor of 4.4 in molecular crystal simulations.
An acceleration factor of 2.8 was achieved in liquid water simulations at the density function theory level.
Abstract
In molecular dynamics (MD), the accessible time scales are limited by the necessity to choose sufficiently small time steps so that the fastest vibrations of the system can still be modeled. Mass tensor molecular dynamics (MTMD) aims to increase the time step by augmenting the Hamiltonian with a position-dependent mass matrix. Higher masses are assigned to modes with fast vibrations. These modes are identified by using an approximate Hessian matrix. The approximate Hessian matrix presented in this paper is applicable to the simulation of molecular systems, where no changes in the bonding pattern occur. We have adapted the MTMD method to variable cell shape systems and present a suitable symplectic integrator. The efficiency of the method is demonstrated for a system of molecular crystals consisting of N-(4-Methylbenzylidene)-4-methylaniline, where we could sample transitions between two…
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Taxonomy
TopicsForce Microscopy Techniques and Applications · Protein Structure and Dynamics · Origins and Evolution of Life