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Volume 13, Issue 1
DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi

Lane W. Votapka, Luke Czapla, Maxim Zhenirovskyy & Rommie E. Amaro

DOI: 10.4208/cicp.170711.111111s

Commun. Comput. Phys., 13 (2013), pp. 256-268.

Published online: 2013-01

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  • Abstract

A new VMD plugin that interfaces with DelPhi to provide ensemble-averaged 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 explicitly solvated all-atom molecular dynamics trajectories. The differences between the ensemble-averaged electrostatics and those obtained from a single structure are examined in detail for these examples, revealing how the plugin can be a powerful tool in facilitating the modeling of electrostatic interactions in biological systems.

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COPYRIGHT: © Global Science Press

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@Article{CiCP-13-256, author = {Lane W. Votapka, Luke Czapla, Maxim Zhenirovskyy and Rommie E. Amaro}, title = {DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi}, journal = {Communications in Computational Physics}, year = {2013}, volume = {13}, number = {1}, pages = {256--268}, abstract = {

A new VMD plugin that interfaces with DelPhi to provide ensemble-averaged 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 explicitly solvated all-atom molecular dynamics trajectories. The differences between the ensemble-averaged electrostatics and those obtained from a single structure are examined in detail for these examples, revealing how the plugin can be a powerful tool in facilitating the modeling of electrostatic interactions in biological systems.

}, issn = {1991-7120}, doi = {https://doi.org/10.4208/cicp.170711.111111s}, url = {http://global-sci.org/intro/article_detail/cicp/7222.html} }
TY - JOUR T1 - DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi AU - Lane W. Votapka, Luke Czapla, Maxim Zhenirovskyy & Rommie E. Amaro JO - Communications in Computational Physics VL - 1 SP - 256 EP - 268 PY - 2013 DA - 2013/01 SN - 13 DO - http://doi.org/10.4208/cicp.170711.111111s UR - https://global-sci.org/intro/article_detail/cicp/7222.html KW - AB -

A new VMD plugin that interfaces with DelPhi to provide ensemble-averaged 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 explicitly solvated all-atom molecular dynamics trajectories. The differences between the ensemble-averaged electrostatics and those obtained from a single structure are examined in detail for these examples, revealing how the plugin can be a powerful tool in facilitating the modeling of electrostatic interactions in biological systems.

Lane W. Votapka, Luke Czapla, Maxim Zhenirovskyy and Rommie E. Amaro. (2013). DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi. Communications in Computational Physics. 13 (1). 256-268. doi:10.4208/cicp.170711.111111s
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