DelPhi Suite: New Developments and Review of Functionalities

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.

Keywords: DelPhi; Poisson-Boltzmann equation; computer code parallelization; dielectric constant; electrostatics.

Figure 1

Numerical benchmarks of solving the Linear and Nonlinear PBEs on aprotein with PDB ID: 4UDF using Open MPDelphi. Speedup (top panel) and efficiency (bottom panel). [Color figure can be viewed at wileyonlinelibrary.com]

Figure 2

Numerical benchmark of solving the Linear and Nonlinear PBEs on aprotein with PDB ID: 4UDF using MPI Delphi. Speedup (top panel), efficiency(middle panel) and RAM reduction percentage (bottom panel). [Color figure can be viewed at wileyonlinelibrary.com]

Figure 3

Electrostatic field lines human parechovirus: red and blue correspond to negative and positive polarity, respectively. The modeling was done using PDB ID 5MJV, which contains 180 proteins, including 41,880 residues. The diameter of the whole virus is 298 Å.