Anisotropic atomic motions in molecular dynamics simulations

doi:10.1088/1478-3975/4/2/002

Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations

Conrad J Burden et al 2007 Phys. Biol. 4 79-90 doi: 10.1088/1478-3975/4/2/002

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Conrad J Burden^1,2 and Aaron J Oakley³
¹ Centre for Bioinformation Science, Mathematical Sciences Institute, Australian National University, Canberra, ACT 0200, Australia
² John Curtin School of Medical Research, Australian National University, Canberra, ACT 0200, Australia
³ Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
E-mail: Conrad.Burden@anu.edu.au

Abstract. Molecular dynamics (MD) simulations using empirical force fields are popular for the study of proteins. In this work, we compare anisotropic atomic fluctuations in nanosecond-timescale MD simulations with those observed in an ultra-high-resolution crystal structure of crambin. In order to make our comparisons, we have developed a compact graphical technique for assessing agreement between spatial atomic distributions determined by MD simulations and observed anisotropic temperature factors.

Received 5 February 2007, accepted for publication 21 May 2007
Published 11 June 2007

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Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations

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