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Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

Biochimica et biophysica acta, 2015-05, Vol.1850 (5), p.1041-1058

2015

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Quantifying the effects of lossy compression on energies calculated from molecular dynamics trajectories

Protein science, 2022-12, Vol.31 (12), p.e4511-n/a

2022

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Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

RNA (Cambridge), 2015-09, Vol.21 (9), p.1578-1590

2015

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Improved Generalized Born Solvent Model Parameters for Protein Simulations

Journal of chemical theory and computation, 2013-04, Vol.9 (4), p.2020-2034

2013

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Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation

The journal of physical chemistry. B, 2007-02, Vol.111 (7), p.1846-1857

2007

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Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data

Journal of computational chemistry, 2018-09, Vol.39 (25), p.2110-2117

2018

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Self-Tensioning Aquatic Caddisfly Silk: Ca2+-Dependent Structure, Strength, and Load Cycle Hysteresis

Biomacromolecules, 2013-10, Vol.14 (10), p.3668-3681

2013

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A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations

The Journal of chemical physics, 2020-08, Vol.153 (5), p.054123-054123

2020

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prepareforleap: An automated tool for fast PDB‐to‐parameter generation

Journal of computational chemistry, 2022-05, Vol.43 (13), p.930-935

2022

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MPI‐parallelization of the grid inhomogeneous solvation theory calculation

Journal of computational chemistry, 2024-04, Vol.45 (10), p.633-637

2024

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Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods

The journal of physical chemistry. B, 2014-04, Vol.118 (13), p.3543-3552

2014

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AmberTools

Journal of chemical information and modeling, 2023-10, Vol.63 (20), p.6183-6191

2023

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On the absence of intrahelical DNA dynamics on the μs to ms timescale

Nature communications, 2014-10, Vol.5 (1), p.5152-5152, Article 5152

2014

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Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory

Journal of chemical theory and computation, 2021-05, Vol.17 (5), p.2714-2724

2021

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k‑Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations

Journal of chemical theory and computation, 2024-07, Vol.20 (13), p.5583-5597

2024

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Improving the speed of volumetric density map generation via cubic spline interpolation

Journal of molecular graphics & modelling, 2021-05, Vol.104, p.107832-107832, Article 107832

2021

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Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber

Journal of chemical theory and computation, 2010-03, Vol.6 (3), p.607-624

2010

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Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

Journal of chemical theory and computation, 2014-01, Vol.10 (1), p.492-499

2014

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Protonation state of the selectivity filter of bacterial voltage‐gated sodium channels is modulated by ions

Proteins, structure, function, and bioinformatics, 2020-03, Vol.88 (3), p.527-539

2020

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Evaluation of DOCK 6 as a pose generation and database enrichment tool

Journal of computer-aided molecular design, 2012-06, Vol.26 (6), p.749-773

2012

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Reliable Oligonucleotide Conformational Ensemble Generation in Explicit Solvent for Force Field Assessment Using Reservoir Replica Exchange Molecular Dynamics Simulations

The journal of physical chemistry. B, 2013-04, Vol.117 (15), p.4014-4027

2013

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Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations

Journal of chemical information and modeling, 2016-07, Vol.56 (7), p.1282-1291

2016

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Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA

The journal of physical chemistry. B, 2017-01, Vol.121 (3), p.451-462

2017

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

Journal of chemical theory and computation, 2007-03, Vol.3 (2), p.557-568

2007

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The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis

Computing in science & engineering, 2015-03, Vol.17 (2), p.30-39

2015

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Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

Quantifying the effects of lossy compression on energies calculated from molecular dynamics trajectories

Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields

Improved Generalized Born Solvent Model Parameters for Protein Simulations

Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation

Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data

Self-Tensioning Aquatic Caddisfly Silk: Ca2+-Dependent Structure, Strength, and Load Cycle Hysteresis

A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations

prepareforleap: An automated tool for fast PDB‐to‐parameter generation

MPI‐parallelization of the grid inhomogeneous solvation theory calculation

Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods

AmberTools

On the absence of intrahelical DNA dynamics on the μs to ms timescale

Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory

k‑Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations

Improving the speed of volumetric density map generation via cubic spline interpolation

Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

Protonation state of the selectivity filter of bacterial voltage‐gated sodium channels is modulated by ions

Evaluation of DOCK 6 as a pose generation and database enrichment tool

Reliable Oligonucleotide Conformational Ensemble Generation in Explicit Solvent for Force Field Assessment Using Reservoir Replica Exchange Molecular Dynamics Simulations

Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA

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

The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis

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