DelPhi Suite : New Developments and Review of Functionalities

© 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

Bibliographische Detailangaben
Veröffentlicht in:Journal of computational chemistry. - 1984. - 40(2019), 28 vom: 30. Okt., Seite 2502-2508
1. Verfasser: Li, Chuan (VerfasserIn)
Weitere Verfasser: Jia, Zhe, Chakravorty, Arghya, Pahari, Swagata, Peng, Yunhui, Basu, Sankar, Koirala, Mahesh, Panday, Shailesh Kumar, Petukh, Marharyta, Li, Lin, Alexov, Emil
Format: Online-Aufsatz
Sprache:English
Veröffentlicht: 2019
Zugriff auf das übergeordnete Werk:Journal of computational chemistry
Schlagworte:Journal Article Research Support, N.I.H., Extramural DelPhi Poisson-Boltzmann equation computer code parallelization dielectric constant electrostatics
Beschreibung
Zusammenfassung:© 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
Electrostatic potential, energies, and forces affect virtually any process in molecular biology, however, computing these quantities is a difficult task due to irregularly shaped macromolecules and the presence of water. Here, we report a new edition of the popular software package DelPhi along with describing its functionalities. The new DelPhi is a C++ object-oriented package supporting various levels of multiprocessing and memory distribution. It is demonstrated that multiprocessing results in significant improvement of computational time. Furthermore, for computations requiring large grid size (large macromolecular assemblages), the approach of memory distribution is shown to reduce the requirement of RAM and thus permitting large-scale modeling to be done on Linux clusters with moderate architecture. The new release comes with new features, whose functionalities and applications are described as well. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc
Beschreibung:Date Completed 11.08.2020
Date Revised 20.07.2024
published: Print-Electronic
Citation Status MEDLINE
ISSN:1096-987X
DOI:10.1002/jcc.26006