Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis (Q27334394)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26149645%20AND%20SRC:MED&resulttype=core&format=json

18 February 2020

title

Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis (English)

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18 February 2020

1

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18 February 2020

William F Flynn

2

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18 February 2020

author name string

Emilio Gallicchio

3

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18 February 2020

Bin W Zhang

4

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18 February 2020

Peng He

5

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18 February 2020

Zhiqiang Tan

6

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18 February 2020

Ronald M Levy

7

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18 February 2020

language of work or name

English

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publication date

7 July 2015

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Journal of Computational Chemistry

18 February 2020

published in

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18 February 2020

volume

36

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18 February 2020

page(s)

1772-1785

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18 February 2020

issue

23

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Equilibrium sampling in biomolecular simulations

18 February 2020

cites work

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Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

29 September 2017

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Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).

29 September 2017

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On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities

29 September 2017

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Convergence and error estimation in free energy calculations using the weighted histogram analysis method

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Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

29 September 2017

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Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD).

29 September 2017

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Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2).

29 September 2017

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Alchemical free energy methods for drug discovery: progress and challenges

29 September 2017

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Reaching biological timescales with all-atom molecular dynamics simulations

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Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model

29 September 2017

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29 September 2017

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Error and efficiency of replica exchange molecular dynamics simulations

29 September 2017

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29 September 2017

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29 September 2017

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Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment

29 September 2017

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29 September 2017

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Simple continuous and discrete models for simulating replica exchange simulations of protein folding.

29 September 2017

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Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin.

29 September 2017

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Simulating replica exchange simulations of protein folding with a kinetic network model

29 September 2017

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Asynchronous replica exchange for molecular simulations

29 September 2017

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COMPUTING: Screen Savers of the World Unite!

29 September 2017

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Coupling of replica exchange simulations to a non-Boltzmann structure reservoir

29 September 2017

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Replica exchange with solute tempering: a method for sampling biological systems in explicit water

29 September 2017

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Multiplexed-replica exchange molecular dynamics method for protein folding simulation

29 September 2017

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Escaping free-energy minima

29 September 2017

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29 September 2017

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29 September 2017

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29 September 2017

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Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer.

29 September 2017

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2 June 2018

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2 June 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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Distributed Replica Sampling.

21 January 2018

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21 January 2018

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Resolution exchange simulation.

21 January 2018

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Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes.

21 January 2018

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Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics.

21 January 2018

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Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential.

21 January 2018

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Optimization of replica exchange molecular dynamics by fast mimicking

21 January 2018

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Optimized parallel tempering simulations of proteins.

21 January 2018

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Comparison of sampling efficiency between simulated tempering and replica exchange

21 January 2018

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Replica exchange with guided annealing for accelerated sampling of disordered protein conformations.

21 January 2018

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An infinite swapping approach to the rare-event sampling problem.

21 January 2018

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Infinite swapping replica exchange molecular dynamics leads to a simple simulation patch using mixture potentials.

21 January 2018

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Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing

21 January 2018

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Convergence of replica exchange molecular dynamics.

21 January 2018

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A Second Look at Canonical Sampling of Biomolecules using Replica Exchange Simulation

21 January 2018

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AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

21 January 2018

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On Information and Sufficiency

21 January 2018

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Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape

21 January 2018

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Multidimensional replica-exchange method for free-energy calculations

21 January 2018

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Ab Initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations

21 January 2018

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Two-dimensional replica-exchange method for predicting protein-ligand binding structures

21 January 2018

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Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir

21 January 2018

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12 December 2020

Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent

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12 December 2020

A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling

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12 December 2020

Exchange frequency in replica exchange molecular dynamics

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An improved replica-exchange sampling method: temperature intervals with global energy reassignment

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12 December 2020

Enhancing QM/MM molecular dynamics sampling in explicit environments via an orthogonal-space-random-walk-based strategy

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12 December 2020

Optimized Monte Carlo data analysis

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How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach

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Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations

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12 December 2020

Identifiers

DOI

10.1002/JCC.23996

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26149645%20AND%20SRC:MED&resulttype=core&format=json

18 February 2020

DBLP publication ID

journals/jcc/XiaFGZHTL15

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26149645%20AND%20SRC:MED&resulttype=core&format=json

18 February 2020

1 reference