Sampling the Denatured State of Polypeptides in Water, Urea, and Guanidine Chloride to Strict Equilibrium Conditions with the Help of Massively Parallel Computers

2014 ◽  
Vol 10 (2) ◽  
pp. 846-854 ◽  
Author(s):  
Roberto Meloni ◽  
Carlo Camilloni ◽  
Guido Tiana
Keyword(s):  
Parallel Computers ◽  
Massively Parallel ◽  
Equilibrium Conditions ◽  
Denatured State ◽  
Massively Parallel Computers ◽  
Guanidine Chloride

The Fast Multipole Method in Canonical Ensemble Dynamics on Massively Parallel Computers

1992 ◽  
Vol 278 ◽  
Author(s):  
Steven R. Lustig ◽  
J.J. Cristy ◽  
D.A. Pensak
Keyword(s):  
Canonical Ensemble ◽  
Yukawa Potential ◽  
Direct Method ◽  
Fast Multipole Method ◽  
Parallel Computers ◽  
Massively Parallel ◽  
Fast Multipole ◽  
Massively Parallel Computers ◽  
Multipole Method ◽  
Execution Times

AbstractThe fast multipole method (FMM) is implemented in canonical ensemble particle simulations to compute non-bonded interactions efficiently with explicit error control. Multipole and local expansions have been derived to implement the FMM efficiently in Cartesian coordinates for soft-sphere (inverse power law), Lennard- Jones, Morse and Yukawa potential functions. Significant reductions in execution times have been achieved with respect to the direct method. For a given number, N, of particles the execution times of the direct method scale asO(N2). The FMM execution times scale asO(N) on sequential workstations and vector processors and asymptotically0(logN) on massively parallel computers. Connection Machine CM-2 and WAVETRACER-DTC parallel FMM implementations execute faster than the Cray-YMP vectorized FMM for ensemble sizes larger than 28k and 35k, respectively. For 256k particle ensembles the CM-2 parallel FMM is 12 times faster than the Cray-YMP vectorized direct method and 2.2 times faster than the vectorized FMM. For 256k particle ensembles the WAVETRACER-DTC parallel FMM is 33 times faster than the Cray-YMP vectorized direct method.

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