SHAKE, rattle, and roll: Efficient constraint algorithms for linked rigid bodies
We present an iterative constraint algorithm, QSHAKE, for use with semirigid molecules in molecular dynamics simulations. The algorithm is based on “SHAKE‐ing” bond constraints between rigid bodies, whose equations of motion are solved in the quaternion framework. The algorithm is derived and its pe...
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| Vydáno v: | Journal of computational chemistry Ročník 19; číslo 1; s. 102 - 111 |
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| Jazyk: | angličtina |
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John Wiley & Sons, Inc
15.01.1998
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| ISSN: | 0192-8651, 1096-987X |
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| Abstract | We present an iterative constraint algorithm, QSHAKE, for use with semirigid molecules in molecular dynamics simulations. The algorithm is based on “SHAKE‐ing” bond constraints between rigid bodies, whose equations of motion are solved in the quaternion framework. The algorithm is derived and its performance compared with SHAKE for liquid octane. QSHAKE is significantly more efficient whenever SHAKE requires triangles (or tetrahedra) of constraints to maintain molecular shape. Efficiencies are gained because QSHAKE reduces the number of holonomic constraints that must be solved iteratively and requires fewer iterations to obtain convergence. The gains in efficiency are most noticeable when a high degree of precision is imposed on the constraint criteria. QSHAKE is also stable at larger time steps than SHAKE, thus allowing for even more efficient exploration of phase space for semirigid molecules. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 102–111, 1998 |
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| AbstractList | We present an iterative constraint algorithm, QSHAKE, for use with semirigid molecules in molecular dynamics simulations. The algorithm is based on “SHAKE‐ing” bond constraints between rigid bodies, whose equations of motion are solved in the quaternion framework. The algorithm is derived and its performance compared with SHAKE for liquid octane. QSHAKE is significantly more efficient whenever SHAKE requires triangles (or tetrahedra) of constraints to maintain molecular shape. Efficiencies are gained because QSHAKE reduces the number of holonomic constraints that must be solved iteratively and requires fewer iterations to obtain convergence. The gains in efficiency are most noticeable when a high degree of precision is imposed on the constraint criteria. QSHAKE is also stable at larger time steps than SHAKE, thus allowing for even more efficient exploration of phase space for semirigid molecules. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 102–111, 1998 |
| Author | Forester, Timothy R. Smith, William |
| Author_xml | – sequence: 1 givenname: Timothy R. surname: Forester fullname: Forester, Timothy R. organization: Department for Computation and Information, CCLRC Daresbury Laboratory, Daresbury, Warrington, Chesire WA4 4AD, United Kingdom – sequence: 2 givenname: William surname: Smith fullname: Smith, William email: w.smith@daresbury.ac.uk organization: Department for Computation and Information, CCLRC Daresbury Laboratory, Daresbury, Warrington, Chesire WA4 4AD, United Kingdom |
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| Cites_doi | 10.1103/PhysRevA.7.1092 10.1016/0021-9991(83)90014-1 10.1103/PhysRevE.50.1559 10.1016/0021-9991(77)90098-5 10.1016/S0263-7855(96)00043-4 10.1080/08927029208022474 10.1063/1.1676585 10.1002/jcc.540070216 |
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| References_xml | – reference: M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, U.K., 1989. – reference: A. Rahman and F. H. Stillinger, J. Chem. Phys., 55, 3336 (1971). – reference: H. Goldstein, Classical Mechanics, 2nd ed., Addison-Wesley, Reading, MA, 1980. – reference: H. C. Andersen, J. Comput. Phys., 54, 24 (1983). – reference: D. Fincham, Mol. Simul., 8, 165 (1992). – reference: D. J. Evans, Mol. Phys., 34, 1745 (1977). – reference: J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Com-put. Phys., 23, 327 (1977). – reference: S. J. Weiner, P. A. Kollman, D. T. Nguyen, and D. A. Case, J. Comput. Chem., 7, 230 (1986). – reference: G. Kneller and K. Hinsen, Phys. Rev. E., 50, 1559 (1994). – reference: J. Barojas, D. Levesque, and B. Quentrec, Phys. Rev., A7, 1092 (1973). – reference: W. Smith and T. R. Forester, J. Mol. Graph., 14, 136 (1996). – volume: 8 start-page: 165 year: 1992 publication-title: Mol. Simul. – volume: 55 start-page: 3336 year: 1971 publication-title: J. Chem. Phys. – volume: 34 start-page: 1745 year: 1977 publication-title: Mol. Phys. – volume: 14 start-page: 136 year: 1996 publication-title: J. Mol. Graph. – volume: 23 start-page: 327 year: 1977 publication-title: J. Com‐put. Phys. – volume: 54 start-page: 24 year: 1983 publication-title: J. Comput. Phys. – year: 1980 – volume: 7 start-page: 230 year: 1986 publication-title: J. Comput. Chem. – volume: A7 start-page: 1092 year: 1973 publication-title: Phys. Rev. – year: 1989 – volume: 50 start-page: 1559 year: 1994 publication-title: Phys. Rev. E. – volume: A7 start-page: 1092 year: 1973 ident: 10.1002/(SICI)1096-987X(19980115)19:1<102::AID-JCC9>3.0.CO;2-T-BIB2 publication-title: Phys. Rev. doi: 10.1103/PhysRevA.7.1092 – volume: 54 start-page: 24 year: 1983 ident: 10.1002/(SICI)1096-987X(19980115)19:1<102::AID-JCC9>3.0.CO;2-T-BIB7 publication-title: J. Comput. Phys. doi: 10.1016/0021-9991(83)90014-1 – volume: 50 start-page: 1559 year: 1994 ident: 10.1002/(SICI)1096-987X(19980115)19:1<102::AID-JCC9>3.0.CO;2-T-BIB8 publication-title: Phys. Rev. E. doi: 10.1103/PhysRevE.50.1559 – volume: 34 start-page: 1745 year: 1977 ident: 10.1002/(SICI)1096-987X(19980115)19:1<102::AID-JCC9>3.0.CO;2-T-BIB3 publication-title: Mol. Phys. – volume-title: Classical Mechanics year: 1980 ident: 10.1002/(SICI)1096-987X(19980115)19:1<102::AID-JCC9>3.0.CO;2-T-BIB9 – volume: 23 start-page: 327 year: 1977 ident: 10.1002/(SICI)1096-987X(19980115)19:1<102::AID-JCC9>3.0.CO;2-T-BIB5 publication-title: J. Com-put. Phys. doi: 10.1016/0021-9991(77)90098-5 – volume: 14 start-page: 136 year: 1996 ident: 10.1002/(SICI)1096-987X(19980115)19:1<102::AID-JCC9>3.0.CO;2-T-BIB10 publication-title: J. Mol. Graph. doi: 10.1016/S0263-7855(96)00043-4 – volume-title: Computer Simulation of Liquids year: 1989 ident: 10.1002/(SICI)1096-987X(19980115)19:1<102::AID-JCC9>3.0.CO;2-T-BIB6 – volume: 8 start-page: 165 year: 1992 ident: 10.1002/(SICI)1096-987X(19980115)19:1<102::AID-JCC9>3.0.CO;2-T-BIB4 publication-title: Mol. Simul. doi: 10.1080/08927029208022474 – volume: 55 start-page: 3336 year: 1971 ident: 10.1002/(SICI)1096-987X(19980115)19:1<102::AID-JCC9>3.0.CO;2-T-BIB1 publication-title: J. Chem. Phys. doi: 10.1063/1.1676585 – volume: 7 start-page: 230 year: 1986 ident: 10.1002/(SICI)1096-987X(19980115)19:1<102::AID-JCC9>3.0.CO;2-T-BIB11 publication-title: J. Comput. Chem. doi: 10.1002/jcc.540070216 |
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| Snippet | We present an iterative constraint algorithm, QSHAKE, for use with semirigid molecules in molecular dynamics simulations. The algorithm is based on “SHAKE‐ing”... |
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| SubjectTerms | bond constraints molecular dynamics simulations QSHAKE semirigid molecules |
| Title | SHAKE, rattle, and roll: Efficient constraint algorithms for linked rigid bodies |
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