Cargando…

Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration

Accelerated molecular dynamics (AMD) is an efficient strategy for accelerating the sampling of molecular dynamics simulations, and observable quantities such as free energies derived on the biased AMD potential can be reweighted to yield results consistent with the original, unmodified potential. In...

Descripción completa

Detalles Bibliográficos
Autores principales:	Fajer, Mikolai, Hamelberg, Donald, McCammon, J. Andrew
Formato:	Texto
Lenguaje:	English
Publicado:	American Chemical Society 2008
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651661/ https://www.ncbi.nlm.nih.gov/pubmed/19461870 http://dx.doi.org/10.1021/ct800250m

Ejemplares similares

w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
por: Arrar, Mehrnoosh, et al.
Publicado: (2012)

Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations
por: de Oliveira, César Augusto F., et al.
Publicado: (2008)

Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations
por: Wereszczynski, Jeff, et al.
Publicado: (2010)

Mechanistic Insight into the Role of Transition-State Stabilization in Cyclophilin A
por: Hamelberg, Donald, et al.
Publicado: (2008)

Thermodynamic and kinetic stability of the Josephin Domain closed arrangement: evidences from replica exchange molecular dynamics
por: Grasso, Gianvito, et al.
Publicado: (2017)

Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant
por: Iwai, Ryosuke, et al.
Publicado: (2018)

Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods
por: Roe, Daniel R., et al.
Publicado: (2014)

Accelerating Solvent Dynamics with Replica Exchange for Improved Free Energy Sampling
por: Darkins, Robert, et al.
Publicado: (2023)

Gaussian Accelerated Molecular Dynamics in NAMD
por: Pang, Yui Tik, et al.
Publicado: (2016)

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics
por: Williams, Sarah L., et al.
Publicado: (2010)

Replica Exchange Molecular Dynamics of Diphenylalanine Amyloid Peptides in Electric Fields
por: Narayan, Brajesh, et al.
Publicado: (2021)

On the Role of Dewetting Transitions in Host–Guest Binding Free Energy Calculations
por: Rogers, Kathleen E., et al.
Publicado: (2012)

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation
por: Miao, Yinglong, et al.
Publicado: (2015)

Accelerated Adaptive Integration Method
por: Kaus, Joseph W., et al.
Publicado: (2014)

Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics
por: Miao, Yinglong, et al.
Publicado: (2014)

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide
por: Bergonzo, Christina, et al.
Publicado: (2013)

Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
por: Wabik, Jacek, et al.
Publicado: (2013)

Cavity Closure of 2-Hydroxypropyl-β-Cyclodextrin: Replica Exchange Molecular Dynamics Simulations
por: Kerdpol, Khanittha, et al.
Publicado: (2019)

Replica exchange molecular dynamics simulation of the coordination of Pt(ii)-Phenanthroline to amyloid-β
por: Turner, Matthew, et al.
Publicado: (2019)

Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics
por: Wang, Yi, et al.
Publicado: (2011)

Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics
por: Grant, Barry J., et al.
Publicado: (2009)

Plasticity of 150-Loop in Influenza Neuraminidase Explored by Hamiltonian Replica Exchange Molecular Dynamics Simulations
por: Han, Nanyu, et al.
Publicado: (2013)

On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations
por: Bucher, Denis, et al.
Publicado: (2011)

Simulations of Biased Agonists in the β(2) Adrenergic Receptor with Accelerated Molecular Dynamics
por: Tikhonova, Irina G., et al.
Publicado: (2013)

Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam
por: Markwick, Phineus R. L., et al.
Publicado: (2011)

Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics
por: Bucher, Denis, et al.
Publicado: (2011)

Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units
por: Lindert, Steffen, et al.
Publicado: (2013)

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation
por: Miao, Yinglong, et al.
Publicado: (2014)

Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering
por: Huang, Kun, et al.
Publicado: (2014)

Editorial: Mechanisms, thermodynamics and kinetics of ligand binding revealed from molecular simulations and machine learning
por: Miao, Yinglong, et al.
Publicado: (2023)

Exchanging Replicas with Unequal Cost, Infinitely and Permanently
por: Roet, Sander, et al.
Publicado: (2022)

Initial Structural Models of the Aβ42 Dimer from Replica Exchange Molecular Dynamics Simulations
por: Blinov, Nikolay, et al.
Publicado: (2017)

Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir
por: Lawrenz, Morgan, et al.
Publicado: (2009)

Molecular dynamics simulations and drug discovery
por: Durrant, Jacob D, et al.
Publicado: (2011)

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics
por: Pierce, Levi C.T., et al.
Publicado: (2012)

Unraveling the structural and molecular properties of 34-residue levans with various branching degrees by replica exchange molecular dynamics simulations
por: Chunsrivirot, Surasak, et al.
Publicado: (2018)

Exploring the Photophysical Properties of Molecular Systems Using Excited State Accelerated ab Initio Molecular Dynamics
por: Ortiz-Sánchez, Juan Manuel, et al.
Publicado: (2012)

Insights into the Folding and Unfolding Processes of Wild-Type and Mutated SH3 Domain by Molecular Dynamics and Replica Exchange Molecular Dynamics Simulations
por: Chu, Wen-Ting, et al.
Publicado: (2013)

Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation
por: de Oliveira, César Augusto F., et al.
Publicado: (2011)

Folding of Trp-cage Mini Protein Using Temperature and Biasing Potential Replica—Exchange Molecular Dynamics Simulations
por: Kannan, Srinivasaraghavan, et al.
Publicado: (2009)

Cannot write session to /tmp/vufind_sessions/sess_058c08at1l4m2cl5got4qts16q