ArticleJournal of chemical theory and computation2019
OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed.
- Article
- Protonation and magnesium ions shape the transition state diversity of phosphoanhydride hydrolysis in water.Nature communications · 2026Article
- MDNA : a software module for DNA structure generation and analysis.Nucleic acids research · 2026Article
- Making PLUMED Fly: A Tutorial on Optimizing Performance.The journal of physical chemistry. B · 2026Article
- Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications.Chemical reviews · 2026Review
- Systematic discovery of disease-modifying targets by prediction from knowledge graph-based AI model and experimental validation: Parkinson's disease case.Computational and structural biotechnology journal · 2026Article
- Iterative variational learning of committor-consistent transition pathways using artificial neural networks.Nature computational science · 2025Article
- WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data.Journal of chemical information and modeling · 2024Article
- Prebiotic chemical reactivity in solution with quantum accuracy and microsecond sampling using neural network potentials.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular Free Energies, Rates, and Mechanisms from Data-Efficient Path Sampling Simulations.Journal of chemical theory and computation · 2023Article
- tICA-Metadynamics for Identifying Slow Dynamics in Membrane Permeation.Journal of chemical theory and computation · 2023Article
- Nonadiabatic Forward Flux Sampling for Excited-State Rare Events.Journal of chemical theory and computation · 2023Article
- Path Sampling Simulations Reveal How the Q61L Mutation Alters the Dynamics of KRas.The journal of physical chemistry. B · 2022Article
- WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications.Journal of chemical theory and computation · 2022Article
- Discovering Collective Variables of Molecular Transitions via Genetic Algorithms and Neural Networks.Journal of chemical theory and computation · 2021Article
- Molecular Understanding of Homogeneous Nucleation of COThe journal of physical chemistry. B · 2021Article
- Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.Chemical reviews · 2020Review
- 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
- Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA.Nucleic acids research · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Transition path sampling techniques allow molecular dynamics simulations of complex systems to focus on rare dynamical events, providing insight into mechanisms and the ability to calculate rates inaccessible by ordinary dynamics simulations. While path sampling algorithms are conceptually as simple as importance sampling Monte Carlo, the technical complexity of their implementation has kept these techniques out of reach of the broad community. Here, we introduce an easy-to-use Python framework called OpenPathSampling (OPS) that facilitates path sampling for (bio)molecular systems with minimal effort and yet is still extensible. Interfaces to OpenMM and an internal dynamics engine for simple models are provided in the initial release, but new molecular simulation packages can easily be added. Multiple ready-to-use transition path sampling methodologies are implemented, including standard transition path sampling (TPS) between reactant and product states and transition interface sampling (TIS) and its replica exchange variant (RETIS), as well as recent multistate and multiset extensions of transition interface sampling (MSTIS, MISTIS). In addition, tools are provided to facilitate the implementation of new path sampling schemes built on basic path sampling components. In this paper, we give an overview of the design of this framework and illustrate the simplicity of applying the available path sampling algorithms to a variety of benchmark problems.
Identifiers
What OpenQuestion holds
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.