Literature DB >> 17476669

Efficient algorithm for "on-the-fly" error analysis of local or distributed serially correlated data.

David R Kent1, Richard P Muller, Amos G Anderson, William A Goddard, Michael T Feldmann.   

Abstract

We describe the Dynamic Distributable Decorrelation Algorithm (DDDA) which efficiently calculates the true statistical error of an expectation value obtained from serially correlated data "on-the-fly," as the calculation progresses. DDDA is an improvement on the Flyvbjerg-Petersen renormalization group blocking method (Flyvberg and Peterson, J Chem Phys 1989, 91, 461). This "on-the-fly" determination of statistical quantities allows dynamic termination of Monte Carlo calculations once a specified level of convergence is attained. This is highly desirable when the required precision might take days or months to compute, but cannot be accurately estimated prior to the calculation. Furthermore, DDDA allows for a parallel implementation which requires very low communication, O(log(2)N), and can also evaluate the variance of a calculation efficiently "on-the-fly." Quantum Monte Carlo calculations are presented to illustrate "on-the-fly" variance calculations for serial and massively parallel Monte Carlo calculations. (c) 2007 Wiley Periodicals, Inc.

Entities:  

Mesh:

Substances:

Year:  2007        PMID: 17476669     DOI: 10.1002/jcc.20746

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  3 in total

1.  Quantifying uncertainty and sampling quality in biomolecular simulations.

Authors:  Alan Grossfield; Daniel M Zuckerman
Journal:  Annu Rep Comput Chem       Date:  2009-01-01

2.  Comparative molecular dynamics study of neuromyelitis optica-immunoglobulin G binding to aquaporin-4 extracellular domains.

Authors:  Domenico Alberga; Daniela Trisciuzzi; Gianluca Lattanzi; Jeffrey L Bennett; Alan S Verkman; Giuseppe Felice Mangiatordi; Orazio Nicolotti
Journal:  Biochim Biophys Acta Biomembr       Date:  2017-05-03       Impact factor: 3.747

3.  Accuracy Test of the OPLS-AA Force Field for Calculating Free Energies of Mixing and Comparison with PAC-MAC.

Authors:  Augustinus J M Sweere; Johannes G E M Fraaije
Journal:  J Chem Theory Comput       Date:  2017-04-24       Impact factor: 6.006

  3 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.