DelPhi Suite: New Developments and Review of Functionalities
| Autor: | Emil Alexov, Swagata Pahari, Yunhui Peng, Chuan Li, Zhe Jia, Sankar Basu, Arghya Chakravorty, Lin Li, Shailesh Kumar Panday, Mahesh Koirala, Marharyta Petukh |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Grid size
Process (engineering) Computer science Computation Static Electricity Software News and Updates Multiprocessing Poisson‐Boltzmann equation computer code parallelization 01 natural sciences Computational science 03 medical and health sciences 0103 physical sciences 030304 developmental biology computer.programming_language 0303 health sciences 010304 chemical physics Suite General Chemistry Software package DelPhi electrostatics Computational Mathematics Task (computing) dielectric constant computer Delphi Software |
| Zdroj: | Journal of Computational Chemistry |
| ISSN: | 1096-987X 0192-8651 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Plný text