Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes

By J. Ryckaert, G. Ciccotti, H. Berendsen. 1977

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Citations in the corpus

• Torsional Diffusion for Molecular Conformer Generation (2022, methodology): “Torsion angle molecular dynamics refers to the range of molecular dynamics methods (Ryckaert et al., 1977; Stein et al., 1997; Chen et al., 2005) using torsion angles instead of Cartesian coordinates as degrees of freedom.”
• Driven to Near-Experimental Accuracy by Refinement via Molecular Dynamics Simulations (2019, methodology): “Bonds involving hydrogen were constrained to be kept rigid with SHAKE method.(41) Langevin dynamics simulations were F IGURE 1 Overall refinement protocol applied by FEIGLAB group in CASP13 HEO ET AL.”
• Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers (2007, methodology): “SHAKE ( 50 ) on bonds involving hydrogens was used in conjunction with an integration step of 2 fs.”