ArticleThe Journal of chemical physics2016
Efficiency in nonequilibrium molecular dynamics Monte Carlo simulations.
Article in The Journal of chemical physics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- pH-Driven βACS omega · 2026Article
- Simulating Biomolecules with the Variable Protonation State: A Tutorial for Constant-pH Molecular Dynamics in NAMD.The journal of physical chemistry. B · 2025Article
- Hybrid neMD/MC lipid swapping algorithm to equilibrate membrane simulation with thermodynamic reservoir.The Journal of chemical physics · 2024Article
- Configurational Sampling of All-Atom Solvated Membranes Using Hybrid Nonequilibrium Molecular Dynamics Monte Carlo Simulations.The journal of physical chemistry letters · 2024Article
- Galvani Offset Potential and Constant-pH Simulations of Membrane Proteins.The journal of physical chemistry. B · 2022Article
- Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials.Journal of chemical theory and computation · 2020Article
- Scalable molecular dynamics on CPU and GPU architectures with NAMD.The Journal of chemical physics · 2020Article
- A remark on the efficiency of the double-system/single-box nonequilibrium approach in the SAMPL6 SAMPLing challenge.Journal of computer-aided molecular design · 2020Article
- A generalized linear response framework for expanded ensemble and replica exchange simulations.The Journal of chemical physics · 2018Article
- Biomolecular Simulations under Realistic Macroscopic Salt Conditions.The journal of physical chemistry. B · 2018Article
- Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.Journal of chemical theory and computation · 2017Article
- Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems.Biophysical reviews · 2017Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Hybrid algorithms combining nonequilibrium molecular dynamics and Monte Carlo (neMD/MC) offer a powerful avenue for improving the sampling efficiency of computer simulations of complex systems. These neMD/MC algorithms are also increasingly finding use in applications where conventional approaches are impractical, such as constant-pH simulations with explicit solvent. However, selecting an optimal nonequilibrium protocol for maximum efficiency often represents a non-trivial challenge. This work evaluates the efficiency of a broad class of neMD/MC algorithms and protocols within the theoretical framework of linear response theory. The approximations are validated against constant pH-MD simulations and shown to provide accurate predictions of neMD/MC performance. An assessment of a large set of protocols confirms (both theoretically and empirically) that a linear work protocol gives the best neMD/MC performance. Finally, a well-defined criterion for optimizing the time parameters of the protocol is proposed and demonstrated with an adaptive algorithm that improves the performance on-the-fly with minimal cost.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.