Fluctuation formulas in molecular-dynamics simulations with the weak coupling heat bath

Morishita, Tetsuya

doi:10.1063/1.1287333

Cited by 164 publications

(174 citation statements)

References 19 publications

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“…10 We briefly describe the weak-coupling algorithm, focusing only on the constant-pressure case. In any Molecular Dynamics algorithm the integrator moves the velocities and positions in a time-step according to the equations of motion:…”

Section: The Reversible Weak-coupling Algorithmmentioning

confidence: 99%

Constant pressure hybrid Molecular Dynamics–Monte Carlo simulations

Faller¹,

Pablo²

2002

The Journal of Chemical Physics

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New hybrid Molecular Dynamics-Monte Carlo methods are proposed to increase the efficiency of constant-pressure simulations. Two variations of the isobaric Molecular Dynamics component of the algorithms are considered. In the first, we use the extended-ensemble method of Andersen ͓H. C. Andersen, J. Chem. Phys. 72, 2384 ͑1980͔͒. In the second, we arrive at a new constant-pressure Monte Carlo technique based on the reversible generalization of the weak-coupling barostat ͓H. J. C. Berendsen et al., J. Chem. Phys. 81, 3684 ͑1984͔͒. This latter technique turns out to be highly effective in equilibrating and maintaining a target pressure. It is superior to the extended-ensemble method, which in turn is superior to simple volume-rescaling algorithms. The efficiency of the proposed methods is demonstrated by studying two systems. The first is a simple Lennard-Jones fluid. The second is a mixture of polyethylene chains of 200 monomers.

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Section: The Reversible Weak-coupling Algorithmmentioning

confidence: 99%

Constant pressure hybrid Molecular Dynamics–Monte Carlo simulations

Faller¹,

Pablo²

2002

The Journal of Chemical Physics

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“…An analogous technique is used in the Berendsen thermostat, for which it was shown that the resulting temperature distribution deviates from the theoretical distribution. 87 The second barostat technique in this work is the algorithm proposed by Martyna, Tuckerman, Tobias and Klein, the MTTK barostat. 39,40 The method can be seen as the natural extension of the Nosé-Hoover and Nosé-Hoover chain thermostat.…”

Section: Barostats Used To Control the Pressurementioning

confidence: 99%

A Comparison of Barostats for the Mechanical Characterization of Metal–Organic Frameworks

Rogge

Vanduyfhuys

Ghysels

et al. 2015

J. Chem. Theory Comput.

168

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In this paper, three barostat coupling schemes for pressure control, which are commonly used in molecular dynamics simulations, are critically compared to characterise the rigid MOF-5 and the exible MIL-53(Al) metal-organic frameworks. We investigate the performance of the three barostats, the Berendsen, the Martyna-Tuckerman-TobiasKlein (MTTK) and the Langevin coupling methods, in reproducing the cell parameters and the pressure versus volume behaviour in isothermal-isobaric simulations. A thermodynamic integration method is used to construct the free energy pro les as a function of volume at nite temperature. It is observed that the aforementioned static properties are well reproduced with the three barostats. However, for static properties depending nonlinearly on the pressure, the Berendsen barostat might give deviating results as it suppresses pressure uctuations more drastically. Finally, dynamic properties, which *

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“…The advantage of the Berendsen thermostat is that the system is weakly coupled to the external thermal bath [8], which leads to its slow relaxation to the reference temperature. However, the Berendsen thermostat has the shortcoming of not generating a canonical temperature distribution [9].…”

Section: Introductionmentioning

confidence: 99%

Effect of the thermostat in the molecular dynamics simulation on the folding of the model protein chignolin

Fuzo

Degrève

2011

J Mol Model

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Molecular dynamics simulations of the model protein chignolin with explicit solvent were carried out, in order to analyze the influence of the Berendsen thermostat on the evolution and folding of the peptide. The dependence of the peptide behavior on temperature was tested with the commonly employed thermostat scheme consisting of one thermostat for the protein and another for the solvent. The thermostat coupling time of the protein was increased to infinity, when the protein is not in direct contact with the thermal bath, a situation known as minimally invasive thermostat. In agreement with other works, it was observed that only in the last situation the instantaneous temperature of the model protein obeys a canonical distribution. As for the folding studies, it was shown that, in the applications of the commonly utilized thermostat schemes, the systems are trapped in local minima regions from which it has difficulty escaping. With the minimally invasive thermostat the time that the protein needs to fold was reduced by two to three times. These results show that the obstacles to the evolution of the extended peptide to the folded structure can be overcome when the temperature of the peptide is not directly controlled.

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Fluctuation formulas in molecular-dynamics simulations with the weak coupling heat bath

Cited by 164 publications

References 19 publications

Constant pressure hybrid Molecular Dynamics–Monte Carlo simulations

Constant pressure hybrid Molecular Dynamics–Monte Carlo simulations

A Comparison of Barostats for the Mechanical Characterization of Metal–Organic Frameworks

Effect of the thermostat in the molecular dynamics simulation on the folding of the model protein chignolin

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