Replica-Exchange Molecular Dynamics Simulations for Various Constant Temperature Algorithms
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- Type
- article
- Published
- 2010-04-12
- Cited by
- 28
- References
- 24
- Access
- Open access
- OpenAlex
- https://openalex.org/W2012965265
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:118456049
Keywords
Replica, Thermostat, Momentum (technical analysis), Molecular dynamics, Statistical physics
References
- Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles.
- The isothermal/isobaric molecular dynamics ensemble
- An Improved Symplectic Integrator for Nosé-Poincaré Thermostat
- Operator-splitting integrators for constant-temperature molecular dynamics
- Canonical dynamics: Equilibrium phase-space distributions.
- Exchange Monte Carlo Method and Application to Spin Glass Simulations
- A unified formulation of the constant temperature molecular dynamics methods
- High-strain-rate plastic flow studied via nonequilibrium molecular dynamics
- VMD: visual molecular dynamics.
- Quasisymplectic integrators for stochastic differential equations.
- The Nosé-Poincaré Method for Constant Temperature Molecular Dynamics
- Replica-exchange molecular dynamics method for protein folding
- A molecular dynamics method for simulations in the canonical ensemble
- Computer Simulation of Liquids
- Computer ‘‘experiment’’ for nonlinear thermodynamics of Couette flow
- Generalized-ensemble algorithms for molecular simulations of biopolymers.
- An efficient newton‐like method for molecular mechanics energy minimization of large molecules
- How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
- Explicit reversible integrators for extended systems dynamics
- Molecular dynamics simulations at constant pressure and/or temperature
Cited by
- Protein folding simulations by generalized-ensemble algorithms.
- Protein Conformational Dynamics
- GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
- Enhanced sampling algorithms.
- Comparison of Replica-Permutation Molecular Dynamics Simulations with and without Detailed Balance Condition
- On the use of a weak-coupling thermostat in replica-exchange molecular dynamics simulations.
- Mass-scaling replica-exchange molecular dynamics optimizes computational resources with simpler algorithm.
- Generalised-ensemble algorithms for studying temperature and pressure dependence of complex systems
- Generalized-Ensemble Algorithms for the Isobaric–Isothermal Ensemble
- Molecular simulations in generalised ensemble
- Free-energy analysis of water affinity in polymer studied by atomistic molecular simulation combined with the theory of solutions in the energy representation.
- Molecular dynamics of the structural changes of helical peptides induced by pressure
- Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms
- Momentum and Velocity Scaling Rules in Replica-Exchange Molecular Dynamics Simulations with Mass Manipulation
- Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems.
- Ligand docking simulations by generalized-ensemble algorithms.
- On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics
- General Formalism of Mass Scaling Approach for Replica-Exchange Molecular Dynamics and its Application
- Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study
- Implementation of replica-exchange umbrella sampling in GAMESS
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- Further cautionary tales on thermostatting in Molecular Dynamics: energy equipartitioning and non-equilibrium processes in gas-phase simulations