Abstract
A block version of the Shake method for heavy atom simulation in biological systems is presented in this paper. The method solves successively, independent blocks of constraints of small size by a Newton method. This algorithm is implemented in TAKAKAW, an efficient parallel molecular dynamics code. This method has been tested on a small system and on an ionic canal of 67671 atoms.
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Coulaud, O., Bernard, PE. Parallel constrained molecular dynamics. Numerical Algorithms 24, 393–405 (2000). https://doi.org/10.1023/A:1019170032549
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DOI: https://doi.org/10.1023/A:1019170032549