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Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules

https://doi.org/10.1021/ct500874p
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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.20289openalex-snapshot
Scalable molecular dynamics with NAMD
inferredcites →https://doi.org/10.1002/jcc.20652openalex-snapshot
Characterization of conformational equilibria through Hamiltonian and temperature replica‐exchange simulations: Assessing entropic and environmental effects
inferredcites →https://doi.org/10.1002/jcc.21285openalex-snapshot
Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics
inferredcites →https://doi.org/10.1002/wcms.1157openalex-snapshot
Frontiers in free‐energy calculations of biological systems
inferredcites →https://doi.org/10.1007/978-3-540-38448-9openalex-snapshot
Free Energy Calculations
inferredcites →https://doi.org/10.1007/s00205-011-0426-yopenalex-snapshot
Long-Time Convergence of an Adaptive Biasing Force Method: The Bi-Channel Case
inferredcites →https://doi.org/10.1016/0009-2614(84)80098-6openalex-snapshot
Stochastic boundary conditions for molecular dynamics simulations of ST2 water
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/j.bpj.2014.03.007openalex-snapshot
Unknown Unknowns: the Challenge of Systematic and Statistical Error in Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1016/j.cpc.2013.12.014openalex-snapshot
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD
inferredcites →https://doi.org/10.1016/s0009-2614(99)01123-9openalex-snapshot
Replica-exchange molecular dynamics method for protein folding
inferredcites →https://doi.org/10.1021/ct1001768openalex-snapshot
Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations
inferredcites →https://doi.org/10.1021/ct200726vopenalex-snapshot
Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering
inferredcites →https://doi.org/10.1021/ct3008099openalex-snapshot
Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
inferredcites →https://doi.org/10.1021/ct5002076openalex-snapshot
Thermodynamics of Deca-alanine Folding in Water
inferredcites →https://doi.org/10.1021/ct500874popenalex-snapshot
Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules
inferredcites →https://doi.org/10.1021/ct9004432openalex-snapshot
Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables
inferredcites →https://doi.org/10.1021/ct900524topenalex-snapshot
Potential of Mean Force Calculations: A Multiple-Walker Adaptive Biasing Force Approach
inferredcites →https://doi.org/10.1021/ja036959eopenalex-snapshot
Improved Treatment of the Protein Backbone in Empirical Force Fields
inferredcites →https://doi.org/10.1021/jp0356620openalex-snapshot
The Development of Replica-Exchange-Based Free-Energy Methods
inferredcites →https://doi.org/10.1021/jp075308sopenalex-snapshot
Energetics of Ion Transport in a Peptide Nanotube
inferredcites →https://doi.org/10.1021/jp973084fopenalex-snapshot
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
inferredcites →https://doi.org/10.1063/1.1308516openalex-snapshot
Multidimensional replica-exchange method for free-energy calculations
inferredcites →https://doi.org/10.1063/1.1410978openalex-snapshot
Calculating free energies using average force
inferredcites →https://doi.org/10.1063/1.1570396openalex-snapshot
Reaction paths based on mean first-passage times
inferredcites →https://doi.org/10.1063/1.1642607openalex-snapshot
Assessing the efficiency of free energy calculation methods
inferredcites →https://doi.org/10.1063/1.1773132openalex-snapshot
Overcoming free energy barriers using unconstrained molecular dynamics simulations
inferredcites →https://doi.org/10.1063/1.2711185openalex-snapshot
Computation of free energy profiles with parallel adaptive dynamics
inferredcites →https://doi.org/10.1063/1.2844595openalex-snapshot
Adaptively biased molecular dynamics for free energy calculations
inferredcites →https://doi.org/10.1063/1.3153841openalex-snapshot
Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling
inferredcites →https://doi.org/10.1063/1.462133openalex-snapshot
New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles
inferredcites →https://doi.org/10.1073/pnas.0408098102openalex-snapshot
Reaction coordinates and rates from transition paths
inferredcites →https://doi.org/10.1073/pnas.0810631106openalex-snapshot
Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
inferredcites →https://doi.org/10.1080/00268976.2013.813594openalex-snapshot
Using collective variables to drive molecular dynamics simulations
inferredcites →https://doi.org/10.1080/08927022.2013.841909openalex-snapshot
Achieving ergodic sampling using replica-exchange free-energy calculations
inferredcites →https://doi.org/10.1103/physrevlett.57.2607openalex-snapshot
Replica Monte Carlo Simulation of Spin-Glasses
inferredcites →https://doi.org/10.1142/p579openalex-snapshot
Free Energy Computations
inferredcites →https://doi.org/10.1209/0295-5075/19/6/002openalex-snapshot
Simulated Tempering: A New Monte Carlo Scheme

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