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delensembleelec computing ensemble-averaged electrostatics
Commun. Comput. Phys. Vol. 13, No. 1, pp. 256-268
doi: 10.4208/cicp.170711.111111s January 2013
DelEnsembleElec: Computing Ensemble-Averaged
Electrostatics Using DelPhi
1 1 2
Lane W. Votapka , Luke Czapla , Maxim Zhenirovskyy and
Rommie E. Amaro1,∗
1 Department of Chemistry and Biochemistry, University of California, San Diego,
La Jolla, California 92093, USA.
2 Computational Biophysics and Bioinformatics, Department of Physics, Clemson
University, Clemson, SC 29634, USA.
Received 17 July 2011; Accepted (in revised version) 11 November 2011
Available online 12 June 2012
Abstract. A new VMD plugin that interfaces with DelPhi to provide ensemble-aver-
aged electrostatic calculations using the Poisson-Boltzmann equation is presented. The
general theory and context of this approach are discussed, and examples of the plugin
interface and calculations are presented. This new tool is applied to systems of current
biological interest, obtaining the ensemble-averaged electrostatic properties of the two
major influenza virus glycoproteins, hemagglutinin and neuraminidase, from explic-
itly solvated all-atom molecular dynamics trajectories. The differences between the
ensemble-averaged electrostatics and those obtained from a single structure are exam-
ined in detail for these examples, revealing how the plugin can be a powerful tool in
facilitating the modeling of electrostatic interactions in biological systems.
PACS: 02.70.Ns
Key words: DelEnsembleElec, ensemble-averaged electrostatics, Poisson Boltzmann equation,
DelPhi, molecular dynamics, influenza glycoproteins.
1 Introduction
Electrostat
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