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A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations
Author(s) -
Kräutler Vincent,
van Gunsteren Wilfred F.,
Hünenberger Philippe H.
Publication year - 2001
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/1096-987x(20010415)22:5<501::aid-jcc1021>3.0.co;2-v
Subject(s) - shake , decoupling (probability) , linearization , constraint (computer aided design) , molecular dynamics , lagrange multiplier , cartesian coordinate system , sylvester's law of inertia , mathematics , algorithm , computational chemistry , physics , chemistry , mathematical optimization , nonlinear system , symmetric matrix , quantum mechanics , geometry , eigenvalues and eigenvectors , control engineering , engineering
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