Unified Efficient Thermostat Scheme for the Canonical Ensemble with Holonomic or Isokinetic Constraints via Molecular Dynamics

Zhang, Zhijun; Liu, Xinzijian; Yan, Kangyu; Tuckerman, Mark E.; Liu, Jian

doi:10.1021/acs.jpca.9b02771

Cited by 84 publications

(111 citation statements)

References 90 publications

(264 reference statements)

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“…Large-scale MD simulations on the transition mechanism of MIL-53(Al) were performed using OpenMM 7.5.0 (Eastman et al, 2017), supplemented with the implementation of the new barostat (available online (Vandenhaute, 2021a)). The simulations were performed using a leapfrog Langevin integrator with a friction coefficient of 0.1 ps −1 (Zhang et al, 2019) and a timestep of 0.5 fs. Monte Carlo trial moves in the unit cell degrees of freedom were performed every five steps.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Large-Scale Molecular Dynamics Simulations Reveal New Insights Into the Phase Transition Mechanisms in MIL-53(Al)

2021

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Soft porous crystals have the ability to undergo large structural transformations upon exposure to external stimuli while maintaining their long-range structural order, and the size of the crystal plays an important role in this flexible behavior. Computational modeling has the potential to unravel mechanistic details of these phase transitions, provided that the models are representative for experimental crystal sizes and allow for spatially disordered phenomena to occur. Here, we take a major step forward and enable simulations of metal-organic frameworks containing more than a million atoms. This is achieved by exploiting the massive parallelism of state-of-the-art GPUs using the OpenMM software package, for which we developed a new pressure control algorithm that allows for fully anisotropic unit cell fluctuations. As a proof of concept, we study the transition mechanism in MIL-53(Al) under various external pressures. In the lower pressure regime, a layer-by-layer mechanism is observed, while at higher pressures, the transition is initiated at discrete nucleation points and temporarily induces various domains in both the open and closed pore phases. The presented workflow opens the possibility to deduce transition mechanism diagrams for soft porous crystals in terms of the crystal size and the strength of the external stimulus.

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Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Large-Scale Molecular Dynamics Simulations Reveal New Insights Into the Phase Transition Mechanisms in MIL-53(Al)

2021

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“…29 One more avenue is presented by the inertial extended Lagrangian SCF iteration-free method (iEL/0-SCF). [33][34][35][36]…”

Section: B Generalized Langevin Equation Analysismentioning

confidence: 99%

“…32 Another expansion, which seeks to remain more closely faithful to the original adiabatic dynamics, is the inertial extended Lagrangian SCF iteration-free method (iEL/0-SCF). [33][34][35][36] To be truly useful, a force field must be able to accurately model large and complex condensed phase systems while remaining sufficiently computationally inexpensive to allow extensive statistical sampling with long MD trajectories. Three principal methods are commonly used to model electronic polarization in atomic and molecular systems, induced dipoles, fluctuating charges, and classical Drude oscillators.…”

Section: Introductionmentioning

confidence: 99%

Statistical mechanics of polarizable force fields based on classical Drude oscillators with dynamical propagation by the dual-thermostat extended Lagrangian

Rupakheti

Lamoureux

MacKerell

et al. 2020

The Journal of Chemical Physics

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Polarizable force fields based on classical Drude oscillators offer a practical and computationally efficient avenue to carry out molecular dynamics (MD) simulations of large biomolecular systems. To treat the polarizable electronic degrees of freedom, the Drude model introduces a virtual charged particle that is attached to its parent nucleus via a harmonic spring. Traditionally, the need to relax the electronic degrees of freedom for each fixed set of nuclear coordinates is achieved by performing an iterative self-consistent field (SCF) calculation to satisfy a selected tolerance. This is a computationally demanding procedure that can increase the computational cost of MD simulations by nearly one order of magnitude. To avoid the costly SCF procedure, a small mass is assigned to the Drude particles, which are then propagated as dynamic variables during the simulations via a dual-thermostat extended Lagrangian algorithm. To help clarify the significance of the dual-thermostat extended Lagrangian propagation in the context of the polarizable force field based on classical Drude oscillators, the statistical mechanics of a dual-temperature canonical ensemble is formulated. The conditions for dynamically maintaining the dual-temperature properties in the case of the classical Drude oscillator are analyzed using the generalized Langevin equation.

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“…In this work, we have addressed these issues through careful formulation of an XLMD procedure that utilizes two latent variables -the charge and chemical potential -and enforces the conservation of charge through a holonomic constraint scheme that is conforming for both energy and forces. 23 We have combined this new SCF-less solution for CEM with the Stochastic-XLMD (SXLMD) method for thermostatting, 20 and implemented it within the ReaxFF force field in the Large-scale Atomic and Molecular Massive Parallel Simulation (LAMMPS) library. 24 We show that the stochastic and constrained extended Lagrangian scheme with no iteration, SC-XLMD, is capable of producing stable trajectories over a timescale of nanoseconds, while retaining energy conservation and equivalent thermodynamics properties of the typical CG-SCF solution.…”

Section: Introductionmentioning

confidence: 99%

Stochastic Constrained Extended System Dynamics for Solving Charge Equilibration Models

Tan

Leven

et al. 2020

Preprint

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We present a new stochastic extended Lagrangian solution to charge equilibration that eliminates self-consistent field (SCF) calculations, eliminating the computational bottleneck in solving the many-body solution with standard SCF solvers. By formulating both charges and chemical potential as latent variables, and introducing a holonomic constraint that satisfies charge conservation, the SC-XLMD method accurately reproduces structural, thermodynamic, and dynamics properties using ReaxFF, and shows excellent weak-and strong-scaling performance in the LAMMPS molecular simulation package.

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Unified Efficient Thermostat Scheme for the Canonical Ensemble with Holonomic or Isokinetic Constraints via Molecular Dynamics

Cited by 84 publications

References 90 publications

Large-Scale Molecular Dynamics Simulations Reveal New Insights Into the Phase Transition Mechanisms in MIL-53(Al)

Large-Scale Molecular Dynamics Simulations Reveal New Insights Into the Phase Transition Mechanisms in MIL-53(Al)

Statistical mechanics of polarizable force fields based on classical Drude oscillators with dynamical propagation by the dual-thermostat extended Lagrangian

Stochastic Constrained Extended System Dynamics for Solving Charge Equilibration Models

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