A fast recursive algorithm for molecular dynamics simulation
The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently de...
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| Published in | Journal of computational physics Vol. 106; no. 2; pp. 258 - 268 |
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| Main Authors | , , |
| Format | Journal Article |
| Language | English |
| Published |
Legacy CDMS
Elsevier
01.06.1993
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0021-9991 1090-2716 |
| DOI | 10.1006/jcph.1993.1106 |
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| Abstract | The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues. |
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| AbstractList | The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues. In this paper, we develop a recursive algorithm for solving the dynamical equations of motion for molecular systems. We make use of internal variable models which have been shown to reduce the computation times of molecular dynamics simulations by an order of magnitude when compared with Cartesian models. The O(N) algorithm described in this paper for solving the equations of motion provides additional significant improvements in computational speed. We make extensive use of the spatial operator methods which have been developed recently for the analysis and simulation of the dynamics of multibody systems. The spatial operators are used to derive the equations of motion and obtain an operator expression for the system mass matrix. An alternative square factorization of the mass matrix leads to a closed form expression for its inverse. From this follows the recursive algorithm for computing the generalized accelerations. The computational cost of this algorithm grows only linearly with the number of degrees of freedom. This is in contrast to conventional constrained dynamics algorithms whose cost is a cubic function of the number of degrees of freedom. For the case of a polypeptide molecule with 400 residues, the O(N) algorithm provides computational speedup by a factor of 450 over the conventional O(N[sup 3]) algorithm. We also describe a simplified method for computing and handling the potential function gradients within the dynamics computations. 21 refs., 3 figs. The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations' computation time by an order of magnitude, relative to Cartesian models. Extensive use is made of spatial operator methods recently developed for analysis and simulation of the dynamics of multibody systems. A factor-of-450 speedup over the conventional O(N-cubed) algorithm is demonstrated for the case of a polypeptide molecule with 400 residues. (AIAA) |
| Audience | PUBLIC |
| Author | Vaidehi, N. Rodriguez, G. Jain, A. |
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| Keywords | Freedom degree Equation of motion Molecular structure Molecular dynamics Fast algorithm Dynamic model Recursive algorithm Solution |
| Language | English |
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| Snippet | The present recursive algorithm for solving molecular systems' dynamical equations of motion employs internal variable models that reduce such simulations'... In this paper, we develop a recursive algorithm for solving the dynamical equations of motion for molecular systems. We make use of internal variable models... |
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| StartPage | 258 |
| SubjectTerms | 990200 -- Mathematics & Computers ALGORITHMS CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS COMPUTERIZED SIMULATION DEGREES OF FREEDOM DIFFERENTIAL EQUATIONS DYNAMICS EQUATIONS EQUATIONS OF MOTION Exact sciences and technology FACTORIZATION GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE Inorganic And Physical Chemistry MATHEMATICAL LOGIC Mathematical methods in physics MATRICES MECHANICS Numerical approximation and analysis NUMERICAL SOLUTION PARTIAL DIFFERENTIAL EQUATIONS Physics SIMULATION 661300 -- Other Aspects of Physical Science-- (1992-) |
| Title | A fast recursive algorithm for molecular dynamics simulation |
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