Multicanonical molecular dynamics by variable-temperature thermostats and variable-pressure barostats

Zhang, Cheng; Deem, Michael W.

doi:10.1063/1.4773435

The Journal of Chemical Physics

2013

DOI: 10.1063/1.4773435

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Multicanonical molecular dynamics by variable-temperature thermostats and variable-pressure barostats

Cheng Zhang

Michael W. Deem

Abstract: Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics. These methods use a variable temperature or pressure that is updated on the fly in the thermodynamic controller. These methods are illustrated on a Lennard-Jones system and a structure-based model of proteins.

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Cited by 2 publications

References 51 publications

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Parallel continuous simulated tempering and its applications in large-scale molecular simulations

Zang

Zhang

et al. 2014

The Journal of Chemical Physics

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In this paper, we introduce a parallel continuous simulated tempering (PCST) method for enhanced sampling in studying large complex systems. It mainly inherits the continuous simulated tempering (CST) method in our previous studies [C. Zhang and J. Ma, J. Chem. Phys. 130, 194112 (2009); 132, 244101 (2010)], while adopts the spirit of parallel tempering (PT), or replica exchange method, by employing multiple copies with different temperature distributions. Differing from conventional PT methods, despite the large stride of total temperature range, the PCST method requires very few copies of simulations, typically 2-3 copies, yet it is still capable of maintaining a high rate of exchange between neighboring copies. Furthermore, in PCST method, the size of the system does not dramatically affect the number of copy needed because the exchange rate is independent of total potential energy, thus providing an enormous advantage over conventional PT methods in studying very large systems. The sampling efficiency of PCST was tested in two-dimensional Ising model, LennardJones liquid and all-atom folding simulation of a small globular protein trp-cage in explicit solvent. The results demonstrate that the PCST method significantly improves sampling efficiency compared with other methods and it is particularly effective in simulating systems with long relaxation time or correlation time. We expect the PCST method to be a good alternative to parallel tempering methods in simulating large systems such as phase transition and dynamics of macromolecules in explicit solvent.

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Parallel continuous simulated tempering and its applications in large-scale molecular simulations

Zang

Zhang

et al. 2014

The Journal of Chemical Physics

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Properties prediction and design of self-healing epoxy resin combining molecular dynamics simulation and back propagation neural network

Luo

Jin

Tao

et al. 2021

Mater. Res. Express

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It is difficult to synergistically improve the self-healing and mechanical properties of self-healing epoxy resin system based on Diels-Alder (DA) reversible covalent bond due to its different compositions. In this study, a method combining molecular dynamics (MD) simulation and back propagation (BP) neural network was employed to achieve a balance between self-healing property and mechanical property. In addition, self-healing and mechanical properties were predicted and the influence of different compositions of the system on these properties was investigated by the BP neural network. It was found that the DA bond formed by the furan group of furfuryl glycidyl ether (FGE) and the maleimide group of bismaleimide (BMI) was of great importance for self-healing property, and that diglycidyl ether of bisphenol-A (DGEBA) with a mass fraction of 25%–48% could improve the tensile property of the system. Finally, a self-healing epoxy resin system with superior comprehensive properties was designed through the proposed method under four indexes of Young’s modulus (E), self-healing efficiency ( η ), Ultimate Tensile Strength (UTS), and glass transition temperature (Tg).

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Multicanonical molecular dynamics by variable-temperature thermostats and variable-pressure barostats

Cited by 2 publications

References 51 publications

Parallel continuous simulated tempering and its applications in large-scale molecular simulations

Parallel continuous simulated tempering and its applications in large-scale molecular simulations

Properties prediction and design of self-healing epoxy resin combining molecular dynamics simulation and back propagation neural network

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