DelPhi Suite: New Developments and Review of Functionalities

TLDR

Electrostatic potential, energies, and forces affect virtually any process in molecular biology, but computing these quantities is difficult due to irregularly shaped macromolecules and the presence of water. The authors present a new edition of the DelPhi software package and describe its functionalities. The new DelPhi is a C++ object‑oriented package that supports multiprocessing and memory distribution, and introduces new features whose functionalities and applications are described. Multiprocessing significantly improves computational time, and memory distribution reduces RAM requirements, enabling large‑scale modeling on moderate Linux clusters. © 2019 The Authors; Journal of Computational Chemistry published by Wiley Periodicals, Inc.

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.