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Visualizing Potential Energy Curves and Conformations on Ultra High-Resolution Display Walls

  • In this contribution, we examine how visualization on an ultra high-resolution display wall can augment force-field research in the field of molecular modeling. Accurate force fields are essential for producing reliable simulations, and subsequently important for several fields of applications (e.g. rational drug design and biomolecular modeling). We discuss how using HORNET, a recently constructed specific ultra high-resolution tiled display wall, enhances the visual analytics that are necessary for conformational-based interpretation of the raw data from molecular calculations. Simultaneously viewing multiple potential energy graphs and conformation overlays leads to an enhanced way of evaluating force fields and in their optimization. Consequently, we have integrated visual analytics into our existing Wolf2Pack workflow. We applied this workflow component to analyze how major AMBER force fields (Parm14SB, Gaff, Lipid14, Glycam06j) perform at reproducing the quantum mechanics relative energies and geometries of saturated hydrocarbons. Included in this comparison are the 1996 OPLS force field and our newly developed ExTrM force field. While we focus on atomistic force fields the ideas presented herein are generalizable to other research areas, particularly those that involve numerous representations of large data amounts and whose simultaneous visualization enhances the analysis.

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Metadaten
Document Type:Article
Language:English
Parent Title (English):J Mol Graph Model. (Journal of Molecular Graphics and Modelling)
Volume:62
First Page:174
Last Page:180
ISSN:1093-3263
DOI:https://doi.org/10.1016/j.jmgm.2015.09.014
Pubmed Id:http://www.ncbi.nlm.nih.gov/pubmed?term=26454265
Publisher:Elsevier
Date of first publication:2015/09/21
Note:
The authors would like to acknowledge that this work was partially funded by Germany’s Federal Ministry of Education and Research and the state of North Rhine Westphalia (grant number 03FH005IN3).
Tag:AMBER; Force field; High-resolution displays; Hydrocarbon; Visualization
Departments, institutes and facilities:Fachbereich Informatik
Fachbereich Elektrotechnik, Maschinenbau, Technikjournalismus
Institut für Technik, Ressourcenschonung und Energieeffizienz (TREE)
Institute of Visual Computing (IVC)
Dewey Decimal Classification (DDC):0 Informatik, Informationswissenschaft, allgemeine Werke / 00 Informatik, Wissen, Systeme / 004 Datenverarbeitung; Informatik
Entry in this database:2015/09/29