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A symplectic method for rigid-body molecular simulation

Kol, Ayla
; 
Laird, Brian Bostian
; 
Leimkuhler, Benedict J.
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Abstract
Rigid-body molecular dynamics simulations typically are performed in a quaternion representation. The nonseparable form of the Hamiltonian in quaternions prevents the use of a standard leapfrog (Verlet) integrator, so nonsymplectic Runge–Kutta, multistep, or extrapolation methods are generally used. This is unfortunate since symplectic methods like Verlet exhibit superior energy conservation in long-time integrations. In this article, we describe an alternative method, which we call RSHAKE (for rotation-SHAKE), in which the entire rotation matrix is evolved (using the scheme of McLachlan and Scovel [J. Nonlin. Sci. 16 233 (1995)]) in tandem with the particle positions. We employ a fast approximate Newton solver to preserve the orthogonality of the rotation matrix. We test our method on a system of soft-sphere dipoles and compare with quaternion evolution using a 4th-order predictor–corrector integrator. Although the short-time error of the quaternion algorithm is smaller for fixed time step than that for RSHAKE, the quaternion scheme exhibits an energy drift which is not observed in simulations with RSHAKE, hence a fixed energy tolerance can be achieved by using a larger time step. The superiority of RSHAKE increases with system size.
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This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/107/7/10.1063/1.474596.
Date
1997-06-19
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American Institute of Physics
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Chemistry Scholarly Works
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Kol, Ayla; Laird, Brian Bostian; Leimkuhler, Benedict J. (1997). "A symplectic method for rigid-body molecular simulation." The Journal of Chemical Physics, 107(7):2580-2588. http://dx.doi.org/10.1063/1.474596
URI
https://hdl.handle.net/1808/16149
DOI
10.1063/1.474596
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