On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics

Nagai, Tetsuro; Pantelopulos, George A.; Takahashi, Takuya; Straub, John E.

doi:10.1002/jcc.24430

Cited by 7 publications

(4 citation statements)

References 84 publications

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“…In this way, the position-dependent PMF as well as the position-dependent diffusion constant plays a central role, and we need to obtain these quantities accurately and efficiently from molecular dynamics (MD) simulations. With respect to the PMF (which is also referred to as the free energy landscape and free energy along a reaction coordinate, among other terms), many approaches have been developed and applied to various systems. − In this study, we focus on the methodology to obtain the position-dependent diffusion constant.…”

Section: Introductionmentioning

confidence: 99%

Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement

Nagai

Tsurumaki

Urano

et al. 2020

J. Chem. Theory Comput.

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The authors propose a novel method to evaluate the position-dependent diffusion constant by analyzing unperturbed segments of a trajectory determined by the additional flat-bottom potential. The accuracy of this novel method is first established by studying homogeneous systems, where the reference value can be obtained by the Einstein relation. The applicability of this new method to heterogeneous systems is then demonstrated by studying a hydrophobic solute near a hydrophobic wall. The proposed method is also comprehensively compared with popular conventional methods, whereby the significance of the present method is illustrated. The novel method is powerful and useful for studying kinetics in heterogeneous systems based on molecular dynamics calculations.

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Section: Introductionmentioning

confidence: 99%

Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement

Nagai

Tsurumaki

Urano

et al. 2020

J. Chem. Theory Comput.

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“…Applying a re-weighting method to the multiple trajectories obtained at different temperatures generates a conformational ensemble in an equilibrium state at a target temperature [ 11 , 12 ]. In the past decades, many variant methods of REMD have been developed, e.g., Hamiltonian REMD [ 13 ], surface tension REMD [ 14 ], solute tempering [ 15 , 16 ], and mass scaling REMD [ 17 ]. REMD-based enhanced conformational sampling methods have been applied to investigate the conformational ensembles of a variety of molecular systems in an equilibrium state [ 18 ].…”

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confidence: 99%

Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant

2018

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The replica-exchange molecular dynamics (REMD) method has been used for conformational sampling of various biomolecular systems. To maximize sampling efficiency, some adjustable parameters must be optimized. Although it is agreed that shorter intervals between the replica-exchange attempts enhance traversals in the temperature space, details regarding the artifacts caused by these short intervals are controversial. In this study, we revisit this problem by performing REMD simulations on an alanine octapeptide in an implicit solvent. Fifty different sets of conditions, which are a combination of five replica-exchange periods, five different numbers of replicas, and two thermostat coupling time constants, were investigated. As a result, although short replica-exchange intervals enhanced the traversals in the temperature space, they led to artifacts in the ensemble average of the temperature, potential energy, and helix content. With extremely short replica-exchange intervals, i.e., attempted at every time step, the ensemble average of the temperature deviated from the thermostat temperature by ca. 7 K. Differences in the ensembles were observed even for larger replica-exchange intervals (between 100 and 1,000 steps). In addition, the shorter thermostat coupling time constant reduced the artifacts found when short replica-exchange intervals were used, implying that these artifacts are caused by insufficient thermal relaxation between the replica-exchange events. Our results will be useful to reduce the artifacts found in REMD simulations by adjusting some key parameters.

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“…Many studies in chemistry related with non-additive entropies are available in the literature, for instance [56][57][58][59][60][61][62][63][64][65]. The q-generalization [66,67] of the ubiquitous Arrhenius Law deserves a special mention.…”

Section: (C) Chemistrymentioning

confidence: 99%

Non-additive entropies and statistical mechanics at the edge of chaos: a bridge between natural and social sciences

Tsallis

2023

Phil. Trans. R. Soc. A.

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The Boltzmann–Gibbs (BG) statistical mechanics constitutes one of the pillars of contemporary theoretical physics. It is constructed upon the other pillars—classical, quantum, relativistic mechanics and Maxwell equations for electromagnetism—and its foundations are grounded on the optimization of the BG (additive) entropic functional S BG = − k ∑ i p i ln ⁡ p i . Its use in the realm of classical mechanics is legitimate for vast classes of nonlinear dynamical systems under the assumption that the maximal Lyapunov exponent is positive (currently referred to as strong chaos ), and its validity has been experimentally verified in countless situations. It fails however when the maximal Lyapunov exponent vanishes (referred to as weak chaos ), which is virtually always the case with complex natural, artificial and social systems. To overcome this type of weakness of the BG theory, a generalization was proposed in 1988 grounded on the non-additive entropic functional S q = k ( ( 1 − ∑ i p i q ) / ( q − 1 ) ) ( q ∈ R ; S 1 = S BG ) . The index q and related ones are to be calculated, whenever mathematically tractable, from first principles and reflect the specific class of weak chaos. We review here the basics of this generalization and illustrate its validity with selected examples aiming to bridge natural and social sciences. This article is part of the theme issue ‘Thermodynamics 2.0: Bridging the natural and social sciences (Part 2)’.

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On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics

Cited by 7 publications

References 84 publications

Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement

Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement

Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant

Non-additive entropies and statistical mechanics at the edge of chaos: a bridge between natural and social sciences

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