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Parallel constrained molecular dynamics |
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| Authors: | Olivier Coulaud Pierre-Eric Bernard |
| 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. This revised version was published online in June 2006 with corrections to the Cover Date. |
| Keywords: | molecular dynamics differential algebraic system constraints parallelism Shake algorithm Newton method 65L80 68W10 92-08 92C40 |
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