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A Generalized Non-iterative Matrix Method for Constraint Molecular Dynamics Simulations

✍ Scribed by Makoto Yoneya

Publisher
Elsevier Science
Year
2001
Tongue
English
Weight
87 KB
Volume
172
Category
Article
ISSN
0021-9991

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✦ Synopsis

A generalization of the previously proposed non-iterative matrix method (NIMM) for constraint molecular dynamics simulations is presented. The resultant generalized version of NIMM (gNIMM) makes possible the constraint force calculation with exactly the same procedure (subroutine) for various "Verlet equivalent" integration schemes with the same fourth order of the time step as the constraint error order. This gNIMM needs only the latest available configuration information and does not need extra memory and restart file size to store the one-step earlier configuration as in a previous extension of NIMM by J. Slusher and P. Cummings (1996, Mol. Sim. 18, 213). The method is tested by simulations with systems of fullerenes, a protein, etc., and is three to five times faster than SHAKE for solving the constraints even in such rather large molecule simulations.

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