A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations

2001/01/01 by Vincent Kr�utler, Wilfred F. van Gunsteren, Philippe H. H�nenberger · 11 citations
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Advanced Chemical Physics Studies #DNA and Nucleic Acid Chemistry #Protein Structure and Dynamics

paper · doi:10.1002/1096-987x(20010415)22:5<501::aid-jcc1021>3.0.co;2-v

openalex publication_date 2001/01/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31

Abstract

A common method for the application of distance constraints in molecular simulations employing Cartesian coordinates is the SHAKE procedure for determining the Lagrange multipliers regarding the constraints. This method relies on the linearization and decoupling of the equations governing the atomic coordinate resetting corresponding to each constraint in a molecule, and is thus iterative. In the present study, we consider an alternative method, M-SHAKE, which solves the coupled equations simultaneously by matrix inversion. The performances of the two methods are compared in simulations of the pure solvents water, dimethyl sulfoxide, and chloroform. It is concluded that M-SHAKE is significantly faster than SHAKE when either (1) the molecules contain few distance constraints (solvent), or (2) when a high level of accuracy is required in the application of the constraints. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 501–508, 2001

Citations

• Algorithms for macromolecular dynamics and constraint dynamics
• Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
• LINCS: A linear constraint solver for molecular simulations

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Related

• SHAKE and the exact constraint satisfaction of the dynamics of semi-rigid molecules in Cartesian coordinates, 1973–1977
• LINCS: A linear constraint solver for molecular simulations
• Modeling molecules with constraints
• Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
• ILVES: Accurate and efficient bond length and angle constraints in molecular dynamics