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Algorithm improvements for molecular dynamics simulations
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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/(sici)1096-987x(199906)20:8<786::aid-jcc5>3.0.co;2-bopenalex-snapshot
Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems
inferredcites →https://doi.org/10.1002/1096-987x(20010415)22:5<501::aid-jcc1021>3.0.co;2-vopenalex-snapshot
A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations
inferredcites →https://doi.org/10.1002/jcc.10072openalex-snapshot
Multiple grid methods for classical molecular dynamics
inferredcites →https://doi.org/10.1002/jcc.10120openalex-snapshot
Accelerated Poisson–Boltzmann calculations for static and dynamic systems
inferredcites →https://doi.org/10.1002/jcc.20026openalex-snapshot
Efficient approximate all‐atom solvent accessible surface area method parameterized for folded and denatured protein conformations
inferredcites →https://doi.org/10.1002/jcc.20071openalex-snapshot
A fast pairlist‐construction algorithm for molecular simulations under periodic boundary conditions
inferredcites →https://doi.org/10.1002/jcc.20125openalex-snapshot
A new analytical method for computing solvent‐accessible surface area of macromolecules and its gradients
inferredcites →https://doi.org/10.1002/jcc.20138openalex-snapshot
Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth‐permittivity finite difference Poisson–Boltzmann method
inferredcites →https://doi.org/10.1002/jcc.20197openalex-snapshot
Electrostatic energies and forces computed without explicit interparticle interactions: A linear time complexity formulation
inferredcites →https://doi.org/10.1002/jcc.20211openalex-snapshot
A simple method for faster nonbonded force evaluations
inferredcites →https://doi.org/10.1002/jcc.20240openalex-snapshot
MDS IM A ID : Automatic parameter optimization in fast electrostatic algorithms
inferredcites →https://doi.org/10.1002/jcc.20267openalex-snapshot
A fast, scalable method for the parallel evaluation of distance‐limited pairwise particle interactions
inferredcites →https://doi.org/10.1002/jcc.20274openalex-snapshot
Nonuniform charge scaling (NUCS): A practical approximation of solvent electrostatic screening in proteins
inferredcites →https://doi.org/10.1002/jcc.20290openalex-snapshot
The Amber biomolecular simulation programs
inferredcites →https://doi.org/10.1002/jcc.20692openalex-snapshot
Identification of biomolecular conformations from incomplete torsion angle observations by hidden markov models
inferredcites →https://doi.org/10.1002/jcc.20829openalex-snapshot
Accelerating molecular modeling applications with graphics processors
inferredcites →https://doi.org/10.1002/jcc.20832openalex-snapshot
FACTS: Fast analytical continuum treatment of solvation
inferredcites →https://doi.org/10.1002/jcc.21035openalex-snapshot
Application of MDGRAPE‐3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems
inferredcites →https://doi.org/10.1002/jcc.21169openalex-snapshot
Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations
inferredcites →https://doi.org/10.1002/jcc.21209openalex-snapshot
Accelerating molecular dynamic simulation on graphics processing units
inferredcites →https://doi.org/10.1002/jcc.21237openalex-snapshot
MILCH SHAKE: An efficient method for constraint dynamics applied to alkanes
inferredcites →https://doi.org/10.1002/jcc.21287openalex-snapshot
CHARMM: The biomolecular simulation program
inferredcites →https://doi.org/10.1002/jcc.21357openalex-snapshot
An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions
inferredcites →https://doi.org/10.1002/jcc.21413openalex-snapshot
Efficient nonbonded interactions for molecular dynamics on a graphics processing unit
inferredcites →https://doi.org/10.1002/jcc.21447openalex-snapshot
A GPU solvent–solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software
inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot
CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
inferredcites →https://doi.org/10.1002/jcc.540130805openalex-snapshot
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
inferredcites →https://doi.org/10.1002/jcc.540161003openalex-snapshot
Algorithms for constrained molecular dynamics
inferredcites →https://doi.org/10.1006/jmbi.1997.1284openalex-snapshot
Torsion angle dynamics for NMR structure calculation with the new program Dyana
inferredcites →https://doi.org/10.1007/978-94-015-7658-1_21openalex-snapshot
Interaction Models for Water in Relation to Protein Hydration
inferredcites →https://doi.org/10.1007/s00894-009-0454-9openalex-snapshot
Solvent accessible surface area approximations for rapid and accurate protein structure prediction
inferredcites →https://doi.org/10.1007/s008940100045openalex-snapshot
GROMACS 3.0: a package for molecular simulation and trajectory analysis
inferredcites →https://doi.org/10.1016/0010-4655(91)90021-copenalex-snapshot
Molecular dynamics simulations on distributed memory machines
inferredcites →https://doi.org/10.1016/0010-4655(95)00042-eopenalex-snapshot
GROMACS: A message-passing parallel molecular dynamics implementation
inferredcites →https://doi.org/10.1016/0021-9991(77)90098-5openalex-snapshot
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
inferredcites →https://doi.org/10.1016/0021-9991(83)90014-1openalex-snapshot
Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations
inferredcites →https://doi.org/10.1016/0021-9991(87)90140-9openalex-snapshot
A fast algorithm for particle simulations
inferredcites →https://doi.org/10.1016/j.jcp.2006.05.032openalex-snapshot
P-SHAKE: A quadratically convergent SHAKE in
inferredcites →https://doi.org/10.1016/j.jcp.2006.06.014openalex-snapshot
Zonal methods for the parallel execution of range-limited N-body simulations
inferredcites →https://doi.org/10.1016/j.jcp.2007.05.026openalex-snapshot
“New-version-fast-multipole-method” accelerated electrostatic calculations in biomolecular systems
inferredcites →https://doi.org/10.1016/j.jcp.2008.01.047openalex-snapshot
General purpose molecular dynamics simulations fully implemented on graphics processing units
inferredcites →https://doi.org/10.1016/j.parco.2008.12.005openalex-snapshot
Multilevel summation of electrostatic potentials using graphics processing units
inferredcites →https://doi.org/10.1016/s0010-4655(00)00050-3openalex-snapshot
Parallel atomistic simulations
inferredcites →https://doi.org/10.1016/s0301-4622(98)00226-9openalex-snapshot
Implicit solvent models
inferredcites →https://doi.org/10.1021/ci900455ropenalex-snapshot
High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing
inferredcites →https://doi.org/10.1021/ct600069ropenalex-snapshot
Efficient Generalized Born Models for Monte Carlo Simulations
inferredcites →https://doi.org/10.1021/ct700200bopenalex-snapshot
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
inferredcites →https://doi.org/10.1021/ct700301qopenalex-snapshot
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
inferredcites →https://doi.org/10.1021/ct800557hopenalex-snapshot
Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1021/ct9000685openalex-snapshot
ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
inferredcites →https://doi.org/10.1021/ct900083kopenalex-snapshot
An Adaptive Fast Multipole Boundary Element Method for Poisson−Boltzmann Electrostatics
inferredcites →https://doi.org/10.1021/ct900275yopenalex-snapshot
An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware
inferredcites →https://doi.org/10.1021/ct900463wopenalex-snapshot
Constant Constraint Matrix Approximation: A Robust, Parallelizable Constraint Method for Molecular Simulations
inferredcites →https://doi.org/10.1021/ct900549ropenalex-snapshot
Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models
inferredcites →https://doi.org/10.1021/ct900620bopenalex-snapshot
Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models
inferredcites →https://doi.org/10.1021/ja9090353openalex-snapshot
Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)
inferredcites →https://doi.org/10.1021/jp037421yopenalex-snapshot
Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory
inferredcites →https://doi.org/10.1021/jp0761665openalex-snapshot
Coarse Master Equations for Peptide Folding Dynamics
inferredcites →https://doi.org/10.1021/jp805085yopenalex-snapshot
Optimized Explicit-Solvent Replica Exchange Molecular Dynamics from Scratch
inferredcites →https://doi.org/10.1021/jp961992ropenalex-snapshot
The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii
inferredcites →https://doi.org/10.1021/ma00234a015openalex-snapshot
Effect of constraints on the dynamics of macromolecules
inferredcites →https://doi.org/10.1063/1.1352646openalex-snapshot
Multigrid methods for classical molecular dynamics simulations of biomolecules
inferredcites →https://doi.org/10.1063/1.1478056openalex-snapshot
Flexible constraints: An adiabatic treatment of quantum degrees of freedom, with application to the flexible and polarizable mobile charge densities in harmonic oscillators model for water
inferredcites →https://doi.org/10.1063/1.1743957openalex-snapshot
Phase Transition for a Hard Sphere System
inferredcites →https://doi.org/10.1063/1.2186317openalex-snapshot
Using massively parallel simulation and Markovian models to study protein folding: Examining the dynamics of the villin headpiece
inferredcites →https://doi.org/10.1063/1.2191489openalex-snapshot
The midpoint method for parallelization of particle simulations
inferredcites →https://doi.org/10.1063/1.2431176openalex-snapshot
A common, avoidable source of error in molecular dynamics integrators
inferredcites →https://doi.org/10.1063/1.2714538openalex-snapshot
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
inferredcites →https://doi.org/10.1063/1.2714539openalex-snapshot
Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states
inferredcites →https://doi.org/10.1063/1.3077857openalex-snapshot
An optimized replica exchange molecular dynamics method
inferredcites →https://doi.org/10.1063/1.3216567openalex-snapshot
Progress and challenges in the automated construction of Markov state models for full protein systems
inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot
Comparison of simple potential functions for simulating liquid water
inferredcites →https://doi.org/10.1063/1.463137openalex-snapshot
Reversible multiple time scale molecular dynamics
inferredcites →https://doi.org/10.1063/1.470006openalex-snapshot
A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems
inferredcites →https://doi.org/10.1063/1.481393openalex-snapshot
Elastic molecular dynamics with self-consistent flexible constraints
inferredcites →https://doi.org/10.1073/pnas.0307898101openalex-snapshot
Simulations of the role of water in the protein-folding mechanism
inferredcites →https://doi.org/10.1073/pnas.0605166103openalex-snapshot
Order N algorithm for computation of electrostatic interactions in biomolecular systems
inferredcites →https://doi.org/10.1073/pnas.0905466106openalex-snapshot
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
inferredcites →https://doi.org/10.1080/08927020600991161openalex-snapshot
Fast multipole methods for particle dynamics
inferredcites →https://doi.org/10.1080/08927029508022012openalex-snapshot
An Efficient, Box Shape Independent Non-Bonded Force and Virial Algorithm for Molecular Dynamics
inferredcites →https://doi.org/10.1088/1742-6596/16/1/041openalex-snapshot
Overview of neutral territory methods for the parallel evaluation of pairwise particle interactions
inferredcites →https://doi.org/10.1089/cmb.2008.0157openalex-snapshot
CUSA and CUDE: GPU-Accelerated Methods for Estimating Solvent Accessible Surface Area and Desolvation
inferredcites →https://doi.org/10.1103/physrev.136.a405openalex-snapshot
Correlations in the Motion of Atoms in Liquid Argon
inferredcites →https://doi.org/10.1109/sc.2006.54openalex-snapshot
Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters
inferredcites →https://doi.org/10.1109/sc.2008.5214716openalex-snapshot
Adapting a message-driven parallel application to GPU-accelerated clusters
inferredcites →https://doi.org/10.1126/science.265.5174.909openalex-snapshot
Fast Algorithms for Classical Physics
inferredcites →https://doi.org/10.1145/1024074.1024075openalex-snapshot
ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics
inferredcites →https://doi.org/10.1145/1188455.1188544openalex-snapshot
Molecular dynamics---Scalable algorithms for molecular dynamics simulations on commodity clusters
inferredcites →https://doi.org/10.1145/1250662.1250664openalex-snapshot
Anton, a special-purpose machine for molecular dynamics simulation
inferredcites →https://doi.org/10.1146/annurev.physchem.51.1.129openalex-snapshot
Generalized Born Models of Macromolecular Solvation Effects
inferredcites →https://doi.org/10.1147/rd.492.0465openalex-snapshot
Custom math functions for molecular dynamics
inferredcites →https://doi.org/10.1177/109434209601000401openalex-snapshot
NAMD: a Parallel, Object-Oriented Molecular Dynamics Program
inferredcites →https://doi.org/10.1260/174830108786231722openalex-snapshot
Message-Passing Implementation of the Data Diffusion Communication Model in Fast Multipole Methods: Large Scale Biomolecular Simulations
inferredcites →https://doi.org/10.1529/biophysj.106.103101openalex-snapshot
Molecular Dynamics Simulations Using Temperature-Enhanced Essential Dynamics Replica Exchange
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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From Side Chains Rattling on Picoseconds to Ensemble Simulations of Protein Folding
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Biomolecular Simulation: A Perspective from High Performance Computing
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Hybrid particle‐field molecular dynamics simulations: Parallelization and benchmarks
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Efficient implementation of periodic boundary conditions in Monte Carlo simulation
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Molecular Dynamics Simulations Using Graphics Processing Units
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High‐throughput molecular dynamics simulations: toward a dynamic view of macromolecular structure
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Programming for scientific computing on peta-scale heterogeneous parallel systems
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Atomistic Modelling of Phosphopeptide Recognition for Modular Domains
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The good, the bad and the user in soft matter simulations
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A study on fullerene as a polymer-assisted antiepileptic drug delivery system: A non-covalent interaction
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A Local Parallel Communication Algorithm for Polydisperse Rigid Body Dynamics
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The fine art of preparing membrane transport proteins for biomolecular simulations: Concepts and practical considerations
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Computational Approaches for Organic Semiconductors: From Chemical and Physical Understanding to Predicting New Materials
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Statistical Analysis on the Performance of Molecular Mechanics Poisson–Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study
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Capturing Surface Coverage Effects in Heterogeneous Catalysis
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Molecular simulations and visualization: introduction and overview
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Structural insights into the mechanism of oxidative activation of heme-free H-NOX from Vibrio cholerae
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MDSLB: A new static load balancing method for parallel molecular dynamics simulations
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Modeling Protein Loop Structure by Cyclic Coordinate Descent-based Approach
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Computer Simulation of Liquids
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From the Preface to the First Edition
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List of Greek Symbols
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List of Roman Symbols
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Statistical mechanics
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Molecular dynamics
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Monte Carlo methods
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Some tricks of the trade
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Parallel simulation
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How to analyse the results
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Advanced Monte Carlo methods
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Rare event simulation
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Nonequilibrium molecular dynamics
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Quantum simulations
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Inhomogeneous fluids
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Computers and computer simulation
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Calculation of forces and torques
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Fourier transforms and series
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Configurational temperature
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In Silico Strategies in Tuberculosis Drug Discovery
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Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model
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A Pre-Docking Filter Based on Image Recognition
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