Adaptive multi-stage integrators for optimal energy conservation in molecular simulations
From MaRDI portal
Publication:1674504
DOI10.1016/j.jcp.2016.09.035zbMath1422.65447arXiv1512.03335OpenAlexW2190914950MaRDI QIDQ1674504
Mario Fernández-Pendás, Elena Akhmatskaya, Jesús María Sanz-Serna
Publication date: 25 October 2017
Published in: Journal of Computational Physics (Search for Journal in Brave)
Full work available at URL: https://arxiv.org/abs/1512.03335
molecular dynamicshybrid Monte Carloadaptive integrationGROMACSmulti-stage integratorsvelocity Verlet
Monte Carlo methods (65C05) Hamilton's equations (70H05) Numerical methods for Hamiltonian systems including symplectic integrators (65P10)
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Cites Work
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- Multiple-time-stepping generalized hybrid Monte Carlo methods
- Molecular modeling and simulation. An interdisciplinary guide
- GSHMC: An efficient method for molecular simulation
- RATTLE: A velocity version of the SHAKE algorithm for molecular dynamics calculations
- Symplectic numerical integrators in constrained Hamiltonian systems
- Common molecular dynamics algorithms revisited: Accuracy and optimal time steps of Störmer-Leapfrog integrators
- Nonlinear resonance artifacts in molecular dynamics simulations
- Randomized Hamiltonian Monte Carlo
- Combining stochastic and deterministic approaches within high efficiency molecular simulations
- Optimal tuning of the hybrid Monte Carlo algorithm
- An ergodic sampling scheme for constrained Hamiltonian systems with applications to molecular dynamics
- Numerical Integrators for the Hybrid Monte Carlo Method
- A Family of Symplectic Integrators: Stability, Accuracy, and Molecular Dynamics Applications
- On the Numerical Integration of Ordinary Differential Equations by Symmetric Composition Methods
- Markov Chain Monte Carlo and Numerical Differential Equations
- Cost of the generalised hybrid Monte Carlo algorithm for free field theory