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Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
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journal
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August 2004 |
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Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
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journal
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October 1992 |
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NAMD2: Greater Scalability for Parallel Molecular Dynamics
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journal
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May 1999 |
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Isothermal-isobaric molecular dynamics simulations with Monte Carlo volume sampling
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journal
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September 1995 |
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Some multistep methods for use in molecular dynamics calculations
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journal
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February 1976 |
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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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journal
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March 1977 |
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Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations
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journal
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October 1983 |
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VMD: Visual molecular dynamics
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journal
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February 1996 |
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Hydration theory for molecular biophysics
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book
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January 2002 |
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Solvation Free Energy of the Peptide Group: Its Model Dependence and Implications for the Additive-Transfer Free-Energy Model of Protein Stability
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journal
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September 2013 |
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Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm
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journal
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January 2004 |
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Discretization errors in molecular dynamics simulations with deterministic and stochastic thermostats
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journal
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December 2010 |
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The Potential Distribution Theorem and Models of Molecular Solutions
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book
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January 2006 |
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Symplectic integrators for Hamiltonian problems: an overview
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journal
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January 1992 |
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Geometric numerical integration illustrated by the Störmer–Verlet method
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journal
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May 2003 |
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MD Simulation of Water Using a Rigid Body Description Requires a Small Time Step to Ensure Equipartition
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journal
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December 2023 |
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Tinker 8: Software Tools for Molecular Design
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journal
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August 2018 |
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Importance of Hydrophilic Hydration and Intramolecular Interactions in the Thermodynamics of Helix–Coil Transition and Helix–Helix Assembly in a Deca-Alanine Peptide
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journal
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December 2015 |
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System Size Dependence of Hydration-Shell Occupancy and Its Implications for Assessing the Hydrophobic and Hydrophilic Contributions to Hydration
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journal
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January 2020 |
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Hydrophilic Interactions Dominate the Inverse Temperature Dependence of Polypeptide Hydration Free Energies Attributed to Hydrophobicity
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journal
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November 2020 |
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Exploring the Temperature−Pressure Phase Diagram of Staphylococcal Nuclease
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journal
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March 1999 |
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Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
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journal
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August 2012 |
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Regularizing Binding Energy Distributions and the Hydration Free Energy of Protein Cytochrome C from All-Atom Simulations
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journal
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August 2012 |
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Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning
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journal
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March 2015 |
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Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations
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journal
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April 2009 |
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Equipartition and the Calculation of Temperature in Biomolecular Simulations
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journal
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May 2010 |
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The missing term in effective pair potentials
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journal
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November 1987 |
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Non-van der Waals Treatment of the Hydrophobic Solubilities of CF 4
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journal
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August 2007 |
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Non-Polarizable Force Field of Water Based on the Dielectric Constant: TIP4P/ε
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journal
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January 2014 |
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Free Energy of Ionic Hydration
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journal
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January 1996 |
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All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
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journal
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April 1998 |
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Molecular Theories and Simulation of Ions and Polar Molecules in Water
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journal
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October 1998 |
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CHARMM36m: an improved force field for folded and intrinsically disordered proteins
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journal
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November 2016 |
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Test of the Monte Carlo Method: Fast Simulation of a Small Ising Lattice
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journal
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June 1970 |
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Molecular Dynamics Study of Liquid Water
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journal
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October 1971 |
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Improved simulation of liquid water by molecular dynamics
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journal
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February 1974 |
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A general purpose model for the condensed phases of water: TIP4P/2005
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journal
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December 2005 |
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Canonical sampling through velocity rescaling
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journal
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January 2007 |
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Role of attractive methane-water interactions in the potential of mean force between methane molecules in water
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journal
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June 2008 |
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Comparison of simple potential functions for simulating liquid water
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journal
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July 1983 |
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Constant pressure molecular dynamics simulation: The Langevin piston method
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journal
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September 1995 |
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Simulation of activation free energies in molecular systems
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journal
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August 1996 |
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Calculation of free‐energy differences from computer simulations of initial and final states
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journal
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August 1996 |
|
Ion sizes and finite-size corrections for ionic-solvation free energies
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journal
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December 1997 |
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Molecular dynamics with rigid bodies: Alternative formulation and assessment of its limitations when employed to simulate liquid water
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journal
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September 2017 |
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Refinement of thermostated molecular dynamics using backward error analysis
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journal
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March 2019 |
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Scalable molecular dynamics on CPU and GPU architectures with NAMD
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journal
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July 2020 |
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Dipole moment fluctuation formulas in computer simulations of polar systems
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journal
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November 1983 |
|
A General Theory of Energy Partition with Applications to Quantum Theory
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journal
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April 1918 |
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Hamiltonians for discrete dynamics
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journal
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September 1994 |
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Shadow mass and the relationship between velocity and momentum in symplectic numerical integration
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journal
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April 2000 |
|
Phase Diagram of Water from Computer Simulation
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journal
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June 2004 |
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How Fast-Folding Proteins Fold
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journal
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October 2011 |
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De Novo Protein Design: Fully Automated Sequence Selection
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journal
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October 1997 |
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On the Origins of the Weak Folding Cooperativity of a Designed ββα Ultrafast Protein FSD-1
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journal
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November 2010 |
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Pressure Denaturation of Staphylococcal Nuclease Studied by Neutron Small-Angle Scattering and Molecular Simulation
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journal
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November 2004 |