SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water molecules. An analytical algorithm, called SETTLE, for resetting the positions and velocities to satisfy the holonomic constraints on the rigid water model is presented. This method is still based on the Cartesian coordinate system and can be used in place of SHAKE and RATTLE. We implemented this algorithm in the SPASMS package of molecular mechanics and dynamics. Several series of molecular dynamics simulations were carried out to examine the performance of the new algorithm in comparison with the original RATTLE method. It was found that SETTLE is of higher accuracy and is faster than RATTLE with reasonable tolerances by three to nine times on a scalar machine. Furthermore, the performance improvement ranged from factors of 26 to 98 on a vector machine since the method presented is not iterative. © 1992 by John Wiley & Sons, Inc.
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References in zbMATH (referenced in 10 articles )
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- Bailey, A.G.; Lowe, C.P.; Sutton, A.P.: Efficient constraint dynamics using MILC SHAKE (2008)
- Berendsen, Herman J. C.: Simulating the physical world. Hierarchical modeling from quantum mechanics to fluid dynamics. (2007)
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- Patra, Michael; Hyvönen, Marja T.; Falck, Emma; Sabouri-Ghomi, Mohsen; Vattulainen, Ilpo; Karttunen, Mikko: Long-range interactions and parallel scalability in molecular simulations (2007) ioport
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- Lee, Sang-Ho; Palmo, Kim; Krimm, Samuel: WIGGLE: a new constrained molecular dynamics algorithm in Cartesian coordinates (2005)
- Ma, Qun; Izaguirre, Jesús A.; Skeel, Robert D.: Verlet-I/R-RESPA/Impulse is limited by nonlinear instabilities (2003)
- Neumaier, Arnold: Molecular modeling of proteins and mathematical prediction of protein structure (1997)