Mass-scaling replica-exchange molecular dynamics optimizes computational resources with simpler algorithm

Tetsuro Nagai; Takuya Takahashi

doi:10.1063/1.4895510

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arXiv · 1405.3484

Mass-scaling replica-exchange molecular dynamics optimizes computational resources with simpler algorithm

Tetsuro Nagai·Takuya Takahashi

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Abstract

We develop a novel method of replica-exchange molecular dynamics (REMD) simulation, mass-scaling REMD (MSREMD) method, which improves trajectory accuracy at high temperatures, and thereby contributes to numerical stability. In addition, the MSREMD method can also simplify a replica-exchange routine by eliminating velocity scaling. As a pilot system, a Lennard-Jones fluid is simulated with the new method. The results show that the MSREMD method improves the trajectory accuracy at high temperatures compared with the conventional REMD method. We analytically demonstrate that the MSREMD simulations can reproduce completely the same trajectories of the conventional REMD ones with shorter time steps at high temperatures in case of the Nosé-Hoover thermostats. Accordingly, we can easily compare the computational costs of the REMD and MSREMD simulations. We conclude that the MSREMD method decreases the instability and optimizes the computational resources with simpler algorithm under the constant trajectory accuracy at all temperatures.

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Tetsuro Nagai, Takuya Takahashi. 2014-05-29. Mass-scaling replica-exchange molecular dynamics optimizes computational resources with simpler algorithm. https://doi.org/10.1063/1.4895510

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