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OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

https://doi.org/10.1021/ct300857j
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jcc.10127openalex-snapshot
Consistent treatment of inter‐ and intramolecular polarization in molecular mechanics calculations
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Empirical force fields for biological macromolecules: Overview and issues
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Scalable molecular dynamics with NAMD
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The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area
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inferredcites →https://doi.org/10.1002/jcc.21209openalex-snapshot
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inferredcites →https://doi.org/10.1002/jcc.21287openalex-snapshot
CHARMM: The biomolecular simulation program
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inferredcites →https://doi.org/10.1002/prot.21123openalex-snapshot
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Isothermal-isobaric molecular dynamics simulations with Monte Carlo volume sampling
inferredcites →https://doi.org/10.1016/0010-4655(96)00016-1openalex-snapshot
Ewald summation techniques in perspective: a survey
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Molecular polarizabilities calculated with a modified dipole interaction
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Accelerating Development and Execution Speed with Just-in-Time GPU Code Generation
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Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm
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General purpose molecular dynamics simulations fully implemented on graphics processing units
inferredcites →https://doi.org/10.1021/acs.jctc.8b00529openalex-snapshot
Tinker 8: Software Tools for Molecular Design
inferredcites →https://doi.org/10.1021/ct2003995openalex-snapshot
A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods
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Generalized Born Model with a Simple, Robust Molecular Volume Correction
inferredcites →https://doi.org/10.1021/ct7001336openalex-snapshot
Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum
inferredcites →https://doi.org/10.1021/ct700301qopenalex-snapshot
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inferredcites →https://doi.org/10.1021/ja00046a032openalex-snapshot
The representation of van der Waals (vdW) interactions in molecular mechanics force fields: potential form, combination rules, and vdW parameters
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Molecular mechanics. The MM3 force field for hydrocarbons. 1
inferredcites →https://doi.org/10.1021/jp027815+openalex-snapshot
Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation
inferredcites →https://doi.org/10.1021/jp0735987openalex-snapshot
Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations
inferredcites →https://doi.org/10.1039/tf945410293bopenalex-snapshot
Bond torsion in the vibrations of the benzene molecule
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Quantum statistics and classical mechanics: Real time correlation functions from ring polymer molecular dynamics
inferredcites →https://doi.org/10.1063/1.1873592openalex-snapshot
Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration
inferredcites →https://doi.org/10.1063/1.1877132openalex-snapshot
Solvation free energies of amino acid side chain analogs for common molecular mechanics water models
inferredcites →https://doi.org/10.1063/1.2978177openalex-snapshot
Statistically optimal analysis of samples from multiple equilibrium states
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inferredcites →https://doi.org/10.1063/1.3607597openalex-snapshot
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inferredcites →https://doi.org/10.1063/1.439486openalex-snapshot
Molecular dynamics simulations at constant pressure and/or temperature
inferredcites →https://doi.org/10.1063/1.469273openalex-snapshot
A generalized reaction field method for molecular dynamics simulations
inferredcites →https://doi.org/10.1063/1.470117openalex-snapshot
A smooth particle mesh Ewald method
inferredcites →https://doi.org/10.1080/08927020701744295openalex-snapshot
Harvesting graphics power for MD simulations
inferredcites →https://doi.org/10.1145/1188455openalex-snapshot
Proceedings of the 2006 ACM/IEEE conference on Supercomputing - SC '06
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Molecular dynamics---Scalable algorithms for molecular dynamics simulations on commodity clusters
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Proceedings of the 34th annual international symposium on Computer architecture
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Molecular Vibrations: The Theory of Infrared and Raman Vibrational Spectra
inferredcites →https://doi.org/10.1201/b16251-15openalex-snapshot
Scalable Molecular Dynamics with NAMD

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ReaDDyMM: Fast Interacting Particle Reaction-Diffusion Simulations Using Graphical Processing Units
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MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
inferred← citeshttps://doi.org/10.1016/j.bpj.2015.10.008openalex-snapshot
CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model
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A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics
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Intramolecular Diffusion in α-Synuclein: It Depends on How You Measure It
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NMR Structural Analysis of Isolated Shaker Voltage-Sensing Domain in LPPG Micelles
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Conformational States of the Cytoprotective Protein Bcl-xL
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Calcium-induced environmental adaptability of the blood protein vitronectin
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Folding@home: Achievements from over 20 years of citizen science herald the exascale era
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Prediction of αIIbβ3 integrin structures along its minimum free energy activation pathway
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AlphaFold2 captures conformational transitions in the voltage-gated channel superfamily
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Meso-Soup: A community approach to building a computational description of the biological mesoscale
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Free energy barriers for TMEA+, TMA+, and BF4- ion diffusion through nanoporous carbon electrodes
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Predict the glass transition temperature and plasticization of β-cyclodextrin/water binary system by molecular dynamics simulation
inferred← citeshttps://doi.org/10.1016/j.carres.2019.02.003openalex-snapshot
Impact of branching on the conformational heterogeneity of the lipopolysaccharide from Klebsiella pneumoniae: Implications for vaccine design
inferred← citeshttps://doi.org/10.1016/j.cej.2022.137126openalex-snapshot
Are nanohedgehogs thirsty? Toward new superhydrophobic and anti-icing carbon nanohorn-polymer hybrid surfaces
inferred← citeshttps://doi.org/10.1016/j.cej.2023.142237openalex-snapshot
Open sensu shaped graphene oxide and modern carbon nanomaterials in translucent hydrophobic and omniphobic surfaces – Insight into wetting mechanisms
inferred← citeshttps://doi.org/10.1016/j.celrep.2016.04.085openalex-snapshot
Formation of Chromosomal Domains by Loop Extrusion
inferred← citeshttps://doi.org/10.1016/j.celrep.2022.111064openalex-snapshot
CaMKII binds both substrates and activators at the active site
inferred← citeshttps://doi.org/10.1016/j.ces.2026.125276openalex-snapshot
In situ milling-media retention enables the continuous preparation of hollow HNS microspheres by coupling acoustic-resonance-assisted ball milling with microfluidics
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What Makes a Kinase Promiscuous for Inhibitors?
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Cancer-cell-derived fumarate suppresses the anti-tumor capacity of CD8+ T cells in the tumor microenvironment
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Highlights of (bio-)chemical tools and visualization software for computational science
inferred← citeshttps://doi.org/10.1016/j.commatsci.2019.05.003openalex-snapshot
Hoobas: A highly object-oriented builder for molecular dynamics
inferred← citeshttps://doi.org/10.1016/j.commatsci.2019.05.026openalex-snapshot
Formalizing atom-typing and the dissemination of force fields with foyer
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2015.11.003openalex-snapshot
Homology modelling and molecular docking studies of human placental cadherin protein for its role in teratogenic effects of anti-epileptic drugs
inferred← citeshttps://doi.org/10.1016/j.compfluid.2015.03.021openalex-snapshot
Computational fluid dynamics simulation based on Hadoop Ecosystem and heterogeneous computing
inferred← citeshttps://doi.org/10.1016/j.cpc.2013.09.018openalex-snapshot
PLUMED 2: New feathers for an old bird
inferred← citeshttps://doi.org/10.1016/j.cpc.2015.01.025openalex-snapshot
OpenMM accelerated MMTK
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Strong scaling of general-purpose molecular dynamics simulations on GPUs
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A domain specific language for performance portable molecular dynamics algorithms
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The MolSSI Driver Interface Project: A framework for standardized, on-the-fly interoperability between computational molecular sciences codes
inferred← citeshttps://doi.org/10.1016/j.cplett.2016.10.015openalex-snapshot
Parallel implementation of approximate atomistic models of the AMOEBA polarizable model
inferred← citeshttps://doi.org/10.1016/j.cplett.2017.02.062openalex-snapshot
New forcefield for water nanodroplet on a graphene surface
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Imidazolylchromanones containing non-benzylic oxime ethers: Synthesis and molecular modeling study of new azole antifungals selective against Cryptococcus gattii
inferred← citeshttps://doi.org/10.1016/j.envres.2022.114832openalex-snapshot
The vitamin D receptor as a potential target for the toxic effects of per- and polyfluoroalkyl substances (PFASs): An in-silico study
inferred← citeshttps://doi.org/10.1016/j.eswa.2023.120235openalex-snapshot
SAPocket: Finding pockets on protein surfaces with a focus towards position and voxel channels
inferred← citeshttps://doi.org/10.1016/j.foodres.2022.111275openalex-snapshot
The bioactivity of prenylated stilbenoids and their structure-activity relationship
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2024.136256openalex-snapshot
Drude2019IDPC polarizable force field reveals structure-function relationship of insulin
inferred← citeshttps://doi.org/10.1016/j.jbc.2024.107427openalex-snapshot
Distinct roles of the major binding residues in the cation-binding pocket of the melibiose transporter MelB
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Controlled asymmetric aggregation advances n → π* electronic transition and charge separation for enhanced photocatalytic hydrogen synthesis
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Efficient implementation of the many-body Reactive Bond Order (REBO) potential on GPU
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Green-engineered clay- and carbon-based composite materials for the adsorption of benzene from air
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The Mechanism and Function of Group II Chaperonins
inferred← citeshttps://doi.org/10.1016/j.jmb.2018.10.014openalex-snapshot
Proton Countertransport and Coupled Gating in the Sarcoplasmic Reticulum Calcium Pump
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Cancer-Associated Mutations Perturb the Disordered Ensemble and Interactions of the Intrinsically Disordered p53 Transactivation Domain
inferred← citeshttps://doi.org/10.1016/j.jmb.2022.167598openalex-snapshot
Molecular Basis for the Cation Selectivity of Salmonella typhimurium Melibiose Permease
inferred← citeshttps://doi.org/10.1016/j.jmgm.2013.12.006openalex-snapshot
MDWiZ: A platform for the automated translation of molecular dynamics simulations
inferred← citeshttps://doi.org/10.1016/j.jmgm.2016.07.008openalex-snapshot
Open source molecular modeling
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Elucidating a chemical defense mechanism of Antarctic sponges: A computational study
inferred← citeshttps://doi.org/10.1016/j.jmgm.2023.108606openalex-snapshot
Interactive molecular dynamics in virtual reality for modelling materials and catalysts
inferred← citeshttps://doi.org/10.1016/j.jmgm.2024.108802openalex-snapshot
NPEX: Never give up protein exploration with deep reinforcement learning
inferred← citeshttps://doi.org/10.1016/j.jmgm.2026.109583openalex-snapshot
Staged computational prioritization of lanmodulin binding-site designs for dysprosium-focused rare-earth separation
inferred← citeshttps://doi.org/10.1016/j.jsb.2024.108061openalex-snapshot
Solid-state NMR MAS CryoProbe enables structural studies of human blood protein vitronectin bound to hydroxyapatite
inferred← citeshttps://doi.org/10.1016/j.molcel.2019.07.007openalex-snapshot
α-Ketoglutarate-Activated NF-κB Signaling Promotes Compensatory Glucose Uptake and Brain Tumor Development
inferred← citeshttps://doi.org/10.1016/j.molstruc.2019.04.007openalex-snapshot
Optimized GPU implementation of Merck Molecular Force Field and Universal Force Field
inferred← citeshttps://doi.org/10.1016/j.sbi.2014.04.002openalex-snapshot
Markov state models of biomolecular conformational dynamics
inferred← citeshttps://doi.org/10.1016/j.sbi.2015.12.002openalex-snapshot
Advances in free-energy-based simulations of protein folding and ligand binding
inferred← citeshttps://doi.org/10.1016/j.sbi.2019.12.018openalex-snapshot
Dynamical reweighting methods for Markov models
inferred← citeshttps://doi.org/10.1016/j.softx.2016.12.002openalex-snapshot
pysimm: A python package for simulation of molecular systems
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Particle-based and meshless methods with Aboria
inferred← citeshttps://doi.org/10.1016/j.str.2017.08.013openalex-snapshot
Structural Characterization of Whirlin Reveals an Unexpected and Dynamic Supramodule Conformation of Its PDZ Tandem
inferred← citeshttps://doi.org/10.1016/j.str.2020.09.009openalex-snapshot
Programmed Trade-offs in Protein Folding Networks
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Structural basis for the association of PLEKHA7 with membrane-embedded phosphatidylinositol lipids
inferred← citeshttps://doi.org/10.1016/j.watres.2023.120944openalex-snapshot
Adsorption and removal of polystyrene nanoplastics from water by green-engineered clays
inferred← citeshttps://doi.org/10.1016/j.xcrp.2025.103041openalex-snapshot
AutoLoop is an autoregressive deep learning method for protein loop prediction with high accuracy
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Molecular dynamics simulations of intrinsically disordered protein regions enable biophysical interpretation of variant-effect predictors
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Protein engineering and the use of molecular modeling and simulation: The case of heterodimeric Fc engineering
inferred← citeshttps://doi.org/10.1016/j.ymeth.2019.11.014openalex-snapshot
Spring Model – Chromatin Modeling Tool Based on OpenMM
inferred← citeshttps://doi.org/10.1021/acs.accounts.6b00285openalex-snapshot
Getting the Right Answers for the Right Reasons: Toward Predictive Molecular Simulations of Water with Many-Body Potential Energy Functions
inferred← citeshttps://doi.org/10.1021/acs.accounts.7b00083openalex-snapshot
Advancing Drug Discovery through Enhanced Free Energy Calculations
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Temperature-Induced Misfolding in Prion Protein: Evidence of Multiple Partially Disordered States Stabilized by Non-Native Hydrogen Bonds
inferred← citeshttps://doi.org/10.1021/acs.biochem.7b00178openalex-snapshot
Asymmetric Anchoring Is Required for Efficient Ω-Loop Opening and Closing in Cytosolic Phosphoenolpyruvate Carboxykinase
inferred← citeshttps://doi.org/10.1021/acs.biochem.9b00031openalex-snapshot
Crystal Structure and Conformational Dynamics of Pyrococcus furiosus Prolyl Oligopeptidase
inferred← citeshttps://doi.org/10.1021/acs.biomac.5c00285openalex-snapshot
Dynamics and Interactions of OmpF Porin in an Asymmetric Bacterial Outer Membrane including LPS, ECA, and CPS
inferred← citeshttps://doi.org/10.1021/acs.chemrestox.9b00030openalex-snapshot
Binding Modes and Metabolism of Caffeine
inferred← citeshttps://doi.org/10.1021/acs.chemrev.2c00060openalex-snapshot
Multifaceted Computational Modeling in Glycoscience
inferred← citeshttps://doi.org/10.1021/acs.chemrev.5b00505openalex-snapshot
An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications
inferred← citeshttps://doi.org/10.1021/acs.chemrev.5b00674openalex-snapshot
Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges
inferred← citeshttps://doi.org/10.1021/acs.chemrev.7b00427openalex-snapshot
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00381openalex-snapshot
Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00485openalex-snapshot
ivis Dimensionality Reduction Framework for Biomacromolecular Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00582openalex-snapshot
Protein Surface Printer for Exploring Protein Domains
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00767openalex-snapshot
FragRep: A Web Server for Structure-Based Drug Design by Fragment Replacement
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00121openalex-snapshot
Protein–Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00801openalex-snapshot
Conserved Water Networks Identification for Drug Design Using Density Clustering Approaches on Positional and Orientational Data
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