Two-dimensional simulated tempering for the isobaric–isothermal ensemble with fast on-the-fly weight determination

Abstract

We propose a method to extend the fast on-the-fly weight determination scheme for simulated tempering to two-dimensional space including not only temperature but also pressure. During the simulated tempering simulation, weight parameters for temperature-update and pressure-update are self-updated independently according to the trapezoidal rule. In order to test the effectiveness of the algorithm, we applied our proposed method to a peptide, chignolin, in explicit water. After setting all weight parameters to zero, the weight parameters were quickly determined during the simulation. The simulation realised a uniform random walk in the entire temperature-pressure space.

GRAPHICAL ABSTRACT

Keywords:

• Generalised-ensemble algorithm
• simulated tempering
• molecular dynamics
• isobaric-isothermal ensemble
• high-pressure denaturation

Acknowledgments

All the computer simulations in this research were performed using supercomputers at Research Center for Computational Science, Okazaki, Japan.

Disclosure statement

No potential conflict of interest was reported by the author(s).