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research article

ddX: Polarizable continuum solvation from small molecules to proteins

Nottoli, Michele
•
Herbst, Michael F.  
•
Mikhalev, Aleksandr
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July 1, 2024
Wiley Interdisciplinary Reviews: Computational Molecular Science

Polarizable continuum solvation models are popular in both, quantum chemistry and in biophysics, though typically with different requirements for the numerical methods. However, the recent trend of multiscale modeling can be expected to blur field-specific differences. In this regard, numerical methods based on domain decomposition (dd) have been demonstrated to be sufficiently flexible to be applied all across these levels of theory while remaining systematically accurate and efficient. In this contribution, we present ddX, an open-source implementation of dd-methods for various solvation models, which features a uniform interface with classical as well as quantum descriptions of the solute, or any hybrid versions thereof. We explain the key concepts of the library design and its application program interface, and demonstrate the use of ddX for integrating into standard chemistry packages. Numerical tests illustrate the performance of ddX and its interfaces. This article is categorized under: Software > Quantum Chemistry Software > Simulation Methods.

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Type
research article
DOI
10.1002/wcms.1726
Scopus ID

2-s2.0-85200026235

Author(s)
Nottoli, Michele

Universität Stuttgart

Herbst, Michael F.  

École Polytechnique Fédérale de Lausanne

Mikhalev, Aleksandr

Skolkovo Institute of Science and Technology

Jha, Abhinav

Universität Stuttgart

Lipparini, Filippo

Università di Pisa

Stamm, Benjamin

Universität Stuttgart

Date Issued

2024-07-01

Published in
Wiley Interdisciplinary Reviews: Computational Molecular Science
Volume

14

Issue

4

Article Number

e1726

Subjects

biophysics

•

continuum solvation

•

COSMO

•

linearized Poisson–Boltzmann

•

polarizable continuum model

•

quantum chemistry

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
MATMAT1  
FunderFunding(s)Grant NumberGrant URL

Deutsche Forschungsgemeinschaft

German Research Foundation

440641818,EXC2075-390740016

Stuttgart Center for Simulation Science

INST 40/575‐1 FUGG

Available on Infoscience
January 24, 2025
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/243544
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