DelPhi Suite: New Developments and Review of Functionalities. Issue 28 (25th June 2019)

• Record Type: Journal Article
• Authors: Li, Chuan; Jia, Zhe; Chakravorty, Arghya; Pahari, Swagata; Peng, Yunhui; Basu, Sankar; Koirala, Mahesh; Panday, Shailesh Kumar; Petukh, Marharyta; Li, Lin; Alexov, Emil
• Is Part Of: Journal of computational chemistry. Volume 40:Issue 28(2019)
• Page Start: 2502
• Page End: 2508
• Publication Date: 2019-06-25
• Subjects: DelPhi -- Poisson‐Boltzmann equation -- electrostatics -- computer code parallelization -- dielectric constant; Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.26006
• Languages: English
• ISSNs: 0192-8651

Abstract

Abstract : 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. Abstract : A new edition of the DelPhi software package is released, which comes with new design for developers and also novel features for users, such as large‐scale calculations, electrostatic force calculations, pKa calculations, and so forth.