A fast mollified impulse method for biomolecular atomistic simulations

DOI10.1016/J.JCP.2016.12.024MaRDI QIDQ1685170zbMATHOpenAlexFDO

Authors L. Fath, Marlis Hochbruck, Chandra Veer Singh

Publication date 13 December 2017

Published in Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jcp.2016.12.024

zbMATH Keywords

resonancesmolecular dynamicshighly oscillatorycorotationmollified impulse method

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Biomechanical solid mechanics (74L15)

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Cites work

• scientific article; zbMATH DE number 1595172 (Why is no real title available?)
• scientific article; zbMATH DE number 1595175 (Why is no real title available?)
• scientific article; zbMATH DE number 1595176 (Why is no real title available?)
• scientific article; zbMATH DE number 1405381 (Why is no real title available?)
• scientific article; zbMATH DE number 5171040 (Why is no real title available?)
• A fast recursive algorithm for molecular dynamics simulation
• Algorithmic challenges in computational molecular biophysics
• Dangers of multiple time step methods
• Fast parallel algorithms for short-range molecular dynamics
• Geometric Numerical Integration
• Implementing molecular dynamics on hybrid high performance computers-short range forces
• Long-Time-Step Methods for Oscillatory Differential Equations
• Molecular modeling and simulation. An interdisciplinary guide.
• Mollified Impulse Methods for Highly Oscillatory Differential Equations
• Multiple time scales in classical and quantum-classical molecular dynamics
• Nonlinear resonance artifacts in molecular dynamics simulations
• Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse method
• RATTLE: A velocity version of the SHAKE algorithm for molecular dynamics calculations
• Simulating Hamiltonian Dynamics
• Targeted Mollified Impulse: A Multiscale Stochastic Integrator for Long Molecular Dynamics Simulations
• Verlet-I/R-RESPA/Impulse is Limited by Nonlinear Instabilities

Cited in

(2)

• Fast iterative method for local steric Poisson-Boltzmann theories in biomolecular solvation
• Targeted Mollified Impulse: A Multiscale Stochastic Integrator for Long Molecular Dynamics Simulations

Describes a project that uses

Uses Software

• CHARMM
• OVITO
• VMD

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