Causal relations in molecular dynamics from the multi-variate autoregressive modelA. Gorecki1, J. Trylska2 and B. Lesyng1, 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
received 16 March 2006; accepted in final form 13 June 2006
published online 5 July 2006
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.
87.15.Aa - Theory and modeling; computer simulation.
31.15.Qg - Molecular dynamics and other numerical methods.
05.45.Tp - Time series analysis.
© EDP Sciences 2006