ArticleThe journal of physical chemistry. B2014
Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems.
Article in The journal of physical chemistry. B, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
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- Entangled Schrödinger Bridge Matching.ArXiv · 2025Article
- Structural and allosteric effects of the membrane-bound PI3Kα H1047R mutation and opportunities for drug discovery.Communications chemistry · 2025Article
- Combining Reactive Quantum-Mechanical Molecular-Dynamics Simulations with Mutagenesis, Crystallography, and Enzyme Kinetics to Reveal Plausible Steps of Isocyanide Hydratase Catalysis.Journal of chemical information and modeling · 2025Article
- Free energy landscape of the PI3Kα C-terminal activation.Computational and structural biotechnology journal · 2024Article
- Path Sampling Simulations Reveal How the Q61L Mutation Alters the Dynamics of KRas.The journal of physical chemistry. B · 2022Article
- Escape dynamics of active particles in multistable potentials.Nature communications · 2021Article
- Dissipation bounds the amplification of transition rates far from equilibrium.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Molecular Understanding of Homogeneous Nucleation of COThe journal of physical chemistry. B · 2021Article
- Rate Prediction for Homogeneous Nucleation of Methane Hydrate at Moderate Supersaturation Using Transition Interface Sampling.The journal of physical chemistry. B · 2020Article
- Catalytic Mechanism of Processive GlfT2: Transition Path Sampling Investigation of Substrate Translocation.ACS omega · 2020Article
- Generalized Moment Correction for Long-Ranged Electrostatics.Journal of chemical theory and computation · 2020Article
- Orbital-Dependent Electronic Friction Significantly Affects the Description of Reactive Scattering of NThe journal of physical chemistry letters · 2019Article
- OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics.Journal of chemical theory and computation · 2019Article
- The FUNPET-a New Hybrid Ion Funnel-Ion Carpet Atmospheric Pressure Interface for the Simultaneous Transmission of a Broad Mass Range.Journal of the American Society for Mass Spectrometry · 2018Article
- On the effect of the thermostat in non-equilibrium molecular dynamics simulations.The European physical journal. E, Soft matter · 2018Article
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3 authors.
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Abstract
When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon desirable properties. However, for stochastic equations of motion (e.g., Langevin dynamics), there is still broad disagreement over which integration algorithms are most appropriate. While multiple desiderata have been proposed throughout the literature, consensus on which criteria are important is absent, and no published integration scheme satisfies all desiderata simultaneously. Additional nontrivial complications stem from simulating systems driven out of equilibrium using existing stochastic integration schemes in conjunction with recently developed nonequilibrium fluctuation theorems. Here, we examine a family of discrete time integration schemes for Langevin dynamics, assessing how each member satisfies a variety of desiderata that have been enumerated in prior efforts to construct suitable Langevin integrators. We show that the incorporation of a novel time step rescaling in the deterministic updates of position and velocity can correct a number of dynamical defects in these integrators. Finally, we identify a particular splitting (related to the velocity Verlet discretization) that has essentially universally appropriate properties for the simulation of Langevin dynamics for molecular systems in equilibrium, nonequilibrium, and path sampling contexts.
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