Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models

Journal of Computational Chemistry - Tập 13 Số 8 - Trang 952-962 - 1992
Shuichi Miyamoto1, Peter A. Kollman1
1Dept. of Pharmaceutical Chemistry, University of California, San Francisco, California 94143

Tóm tắt

AbstractAn 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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Tài liệu tham khảo

10.1002/anie.199009921

10.1146/annurev.bb.18.060189.002243

10.1021/ja00194a007

Straatsma T.P., 1988, J. Chem. Phys., 89, 5879, 10.1063/1.455539

Brooks C.L., 1991, J. Am. Chem. Soc., 113, 2295, 10.1021/ja00006a058

10.1021/ja00005a015

10.1089/ard.1991.1.243

10.1002/bip.360290810

10.1063/1.445869

10.1007/978-94-015-7658-1_21

10.1002/jcc.540121016

10.1063/1.1676585

10.1080/00268977700101761

10.1016/0021-9991(77)90098-5

10.1016/0021-9991(83)90014-1

10.1103/PhysRev.159.98

10.1063/1.442716

D.C.Spellmeyer W.C.Swope E.R.Evensen P.A.Kollman andR.Langridge work in progress.

10.1080/00268977700102571

10.1021/ja00036a015

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Journal of Computational Chemistry

Tập 13 Số 8

952-962

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