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Abstract: An efficient molecular dynamics (MD) algorithm is presented in this paper for biomolecular systems, which incorporates a novel variation on the Fast Multipole Method (FMM) coupled to the reversible Reference System Propagator Algorithm (r-RESPA). A top-down FMM is proposed which calculates multipoles recursively from the top of the box tree instead of from the bottom in Greengard 's original FMM, in an effort to be more efficient for noncubic or nonuniform systems. In addition, the use of ... (Update)
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.... More importantly, they do not conserve energy during MD simulations unless enforcing unusual high accuracy, e.g. 12th order multi poles [10, 128]. Typically, the electrostatic problem comes with usually small distributions of mono pole moments that cause self cancellation;...
.... method [84,86] For solvated systems, fast summation methods have been successfully combined with multiple timestep integration methods [87,88]. Variations of the method given in (3.20) include employing switching functions such as (3.21) to intermolecular (water water)...
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BibTeX entry: (Update)
R. Zhou and B. J. Berne. A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems. J. Phys. Chem., 103:9444--9459, 1995. http://citeseer.ist.psu.edu/zhou95new.html More
@article{ zhou95new,
author = "Ruhong Zhou and Bruce J. Berne",
title = "A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems",
journal = "Journal of Chemical Physics",
volume = "103",
number = "21",
month = "????",
pages = "9444--9459",
year = "1995",
url = "citeseer.ist.psu.edu/zhou95new.html" }
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