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  • Mathematics Subject Classification (1991):65M99, 34C15, 34C40, 70F20, 81Q15, 81V55  (1)
  • generalized ensemble  (1)
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  • 1
    Electronic Resource
    Electronic Resource
    Adaptive accuracy control for Car-Parrinello simulations (1999)
    Springer
    Numerische Mathematik 83 (1999), S. 179-186 
    Details
    ISSN: 0945-3245
    Keywords: Mathematics Subject Classification (1991):65M99, 34C15, 34C40, 70F20, 81Q15, 81V55
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Summary. The Car-Parrinello (CP) approach to ab initio molecular dynamics serves as an approximation to time-dependent Born-Oppenheimer (BO) calculations. It replaces the explicit minimization of the energy functional by a fictitious Newtonian dynamics and therefore introduces an artificial mass parameter $\mu$ which controls the electronic motion. A recent theoretical investigation shows that the CP-error, i.e., the deviation of the CP–solution from the BO-solution decreases like $\mu^{1/2}$ asymptotically. Since the computational effort increases like $\mu^{-1/2}$ , the choice of $\mu$ has to find a compromise between efficiency and accuracy. The asymptotical result is used in this paper to construct an easily implemented algorithm which automatically controls $\mu$ : the parameter $\mu$ is repeatedly adapted during the simulation by choosing $\mu$ as large as possible while pushing an error measure below a user-given tolerance. The performance and reliability of the algorithm is illustrated by a typical example.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002110050445
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble: Efficient conformational analysis of RNA (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1689-1697 
    Details
    ISSN: 0192-8651
    Keywords: hybrid Monte Carlo ; generalized ensemble ; reweighting ; n-butane ; triribonucleotide ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A hybrid Monte Carlo method with adaptive temperature choice is presented that exactly generates the distribution of a mixed-canonical ensemble composed of two canonical ensembles at low and high temperature. The analysis of resulting Markov chains with the reweighting technique shows an efficient sampling of the canonical distribution at low temperature whereas the high temperature component facilitates conformational transitions, which allows shorter simulation times. The algorithm is tested by comparing analytical and numerical results for the small n-butane molecule before simulations are performed for a triribonucleotide. Sampling the complex multiminima energy landscape of this small RNA segment, we observe enforced crossing of energy barriers.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1689-1697, 1998
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    Library Location Call Number Volume/Issue/Year Availability
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    Paper (German National Licenses)
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