PCMSolver: an Application Programming Interface for the Polarizable Continuum Model

نویسندگان

  • Roberto Di Remigio
  • T. Daniel Crawford
  • Luca Frediani
چکیده

The growing complexity of quantum chemical program packages requires that an appropriate strategy be devised to implement new features. Scalability is of paramount importance, but it has become clear that maintainability and extensibil-ity of the code play an equally important role in managing this growing complexity [1]. The use of a modular programming paradigm has been recognized as beneficial in many other scientific computing contexts. New features are isolated into libraries that can be accessed by host programs through a well-defined application programming interface (API). Computational tasks are thus implemented into separate, independent and interchangeable modules. These are developed and tested independently of the particular host program in which they will be used [2, 3]. A well-defined API clearly delimits the boundaries of the functionality offered, thus forcing a programming style and standardisation of the functionality, eventually. When coupled with open-source licensing, modularity is a proper step towards ensuring reproducibility of results from scientific simulation software [4]. Open-source development can fully leverage the benefits of widespread, cloud-based, free, code development services, such as hosted distributed version control systems (DVCSs), continuous integration, code coverage, static and dynamic code analyses, nightly regression testing, public issue tracking, code review and so forth: adoption of a modern code development workflow is easily within reach. It is, of course, true that the above mentioned services are not exclusive prerogatives of open-source projects. However, an open review process of scientific software can often help to establish reproducibility, extensibility and sustainability of the software ecosystem. Open-source software, modular development of new functionalities and full-fledged exploitation of DVCSs ensure a much larger scientific impact. Third-parties can easily contribute to the project: by improving the documentation, by reporting bugs or by actively extending the codebase with new functionality. The description of chemical phenomena in complex environments, such as solutions or proteins, is as challenging as it is important for an accurate prediction of a wide range of properties [5]. Quantum chemistry is nowadays a valuable tool: its

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Modelface: an application programming interface (API) for homology modeling studies using Modeller software

An interactive application, Modelface, was presented for Modeller software based on windows platform. The application is able to run all steps of homology modeling including pdb to fasta generation, running clustal, model building and loop refinement. Other modules of modeler including energy calculation, energy minimization and the ability to make single point mutations in the PDB structures a...

متن کامل

Modelface: an application programming interface (API) for homology modeling studies using Modeller software

An interactive application, Modelface, was presented for Modeller software based on windows platform. The application is able to run all steps of homology modeling including pdb to fasta generation, running clustal, model building and loop refinement. Other modules of modeler including energy calculation, energy minimization and the ability to make single point mutations in the PDB structures a...

متن کامل

Wavelet formulation of the polarizable continuum model. II. Use of piecewise bilinear boundary elements.

The simplicity of dielectric continuum models has made them a standard tool in almost any Quantum Chemistry (QC) package. Despite being intuitive from a physical point of view, the actual electrostatic problem at the cavity boundary is challenging: the underlying boundary integral equations depend on singular, long-range operators. The parametrization of the cavity boundary should be molecular-...

متن کامل

Determination of the absolute redox potential of methyldopa: experimental and simulation methodes

The conditional formal potential, E°′of Methyldopa has been studied by cyclic voltammetry at the surface of activated glassy carbon electrode (AGCE) as the working electrode in different pH phosphate buffered solutions. The experimental Standard redox potential, E°′, of Methyldopa is obtained to be 0.72 mV versus SHE (Standard Hydrogen Electrode). E°′ values have also been calculated with the a...

متن کامل

Polarizable molecular dynamics in a polarizable continuum solvent.

We present, for the first time, scalable polarizable molecular dynamics (MD) simulations within a polarizable continuum solvent with molecular shape cavities and exact solution of the mutual polarization. The key ingredients are a very efficient algorithm for solving the equations associated with the polarizable continuum, in particular, the domain decomposition Conductor-like Screening Model (...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2016