Causal relations in molecular dynamics from 
 the multi-variate autoregressive model

doi:10.1209/epl/i2006-10129-2

Causal relations in molecular dynamics from the multi-variate autoregressive model

A. Gorecki et al 2006 Europhys. Lett. 75 503-509 doi: 10.1209/epl/i2006-10129-2

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A. Gorecki¹, J. Trylska² and B. Lesyng^1,2
¹ Department of Biophysics, Institute of Experimental Physics, Warsaw University Zwirki i Wigury 93, 02-089 Warsaw, Poland
² Interdisciplinary Centre for Mathematical and Computational Modelling Pawinskiego 5A, 02-106 Warsaw, Poland

Abstract. We show that Granger-type causality analysis can be applied to determine correlations between atomic motions. A multivariate autoregressive model and directed transfer functions were applied to analyze the causality in the dynamics of a linear chain of atoms and the malonaldehyde molecule. The presented methodology is promising, can be applied in post-processing of classical and quantum-classical molecular dynamics data, and to study the mechanisms of functioning of biomolecular systems.

PACS numbers: 87.15.Aa, 31.15.Qg, 05.45.Tp

Print publication: Issue 3 (August 2006)
Received 16 March 2006, in final form and accepted for publication 13 June 2006
Published 5 July 2006

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Causal relations in molecular dynamics from the multi-variate autoregressive model

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