Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code

DOI10.1016/j.cpc.2023.108742MaRDI QIDQ6105063

Santiago Marco-Sola, Jesús Alastruey-Benedé, Javier Sancho, Lorién López-Villellas, Pablo García Risueño, Miquel Moretó, Juan José Galano-Frutos, Pablo Ibáñez, Carl Christian Kjelgaard Mikkelsen

Publication date: 26 June 2023

Published in: Computer Physics Communications (Search for Journal in Brave)

zbMATH Keywords

Newton's methodmolecular dynamicsSHAKEnon-linear equationsLINCSconstraint algorithms

Mathematics Subject Classification ID

Numerical analysis (65-XX) Mechanics of particles and systems (70-XX)

Cites Work

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• Mathematical approaches to biomolecular structure and dynamics. Proceedings of the 1994 IMA summer program on molecular biology
• Revisiting and parallelizing SHAKE
• Linearly scaling direct method for accurately inverting sparse banded matrices
• Simulating Hamiltonian Dynamics
• Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations
• Geometric Numerical Integration
• Nonlinear Generalizations of Matrix Diagonal Dominance with Application to Gauss–Seidel Iterations

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