Expanded Functionality and Portability for the Colvars Library

Colvars is an open-source C++ library that provides a modular toolkit for collective-variable-based molecular simulations. It allows practitioners to easily create and implement descriptors that best fit a process of interest and to apply a wide range of biasing algorithms in collective variable space. This paper reviews several features and improvements to Colvars that were added since its original introduction. Special attention is given to contributions that significantly expanded the capabilities of this software or its distribution with major MD simulation packages. Collective variables can now be optimized either manually or by machine-learning methods, and the space of descriptors can be explored interactively using the graphical interface included in VMD. Beyond the spatial coordinates of individual molecules, Colvars can now apply biasing forces to mesoscale structures and alchemical degrees of freedom and perform simulations guided by experimental data within ensemble averages or probability distributions. It also features advanced computational schemes to boost the accuracy, robustness, and general applicability of simulation methods, including extended-system and multiple-walker adaptive biasing force, boundary conditions for metadynamics, replica exchange with biasing potentials, and adiabatic bias molecular dynamics. The library is made available directly within the main distributions of the academic software GROMACS, LAMMPS, NAMD, Tinker-HP, and VMD. The robustness of the software and the reliability of the results are ensured through the use of continuous integration with a test suite within the source repository.

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Publication Details

Journal
The Journal of Physical Chemistry B
Published
2024-11-06
DOI
https://doi.org/10.1021/acs.jpcb.4c05604
Citations
33
Primary Topic
Protein Structure and Dynamics
Type
article
Field-Weighted Citation Impact
7.72

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article

Expanded Functionality and Portability for the Colvars Library

Jérôme Hénin, Axel Kohlmeyer, Giacomo Fiorin, Fabrizio Marinelli et al.
33 citations
The Journal of Physical Chemistry B
Protein Structure and Dynamics
7.72
article

Expanded Functionality and Portability for the Colvars Library

Jérôme Hénin, Axel Kohlmeyer, Giacomo Fiorin, Fabrizio Marinelli, Haochuan Chen, Lucy R. Forrest, Christophe J. Chipot, Hubert Santuz
article en
33 citations

Abstract

Colvars is an open-source C++ library that provides a modular toolkit for collective-variable-based molecular simulations. It allows practitioners to easily create and implement descriptors that best fit a process of interest and to apply a wide range of biasing algorithms in collective variable space. This paper reviews several features and improvements to Colvars that were added since its original introduction. Special attention is given to contributions that significantly expanded the capabilities of this software or its distribution with major MD simulation packages. Collective variables can now be optimized either manually or by machine-learning methods, and the space of descriptors can be explored interactively using the graphical interface included in VMD. Beyond the spatial coordinates of individual molecules, Colvars can now apply biasing forces to mesoscale structures and alchemical degrees of freedom and perform simulations guided by experimental data within ensemble averages or probability distributions. It also features advanced computational schemes to boost the accuracy, robustness, and general applicability of simulation methods, including extended-system and multiple-walker adaptive biasing force, boundary conditions for metadynamics, replica exchange with biasing potentials, and adiabatic bias molecular dynamics. The library is made available directly within the main distributions of the academic software GROMACS, LAMMPS, NAMD, Tinker-HP, and VMD. The robustness of the software and the reliability of the results are ensured through the use of continuous integration with a test suite within the source repository.

The Journal of Physical Chemistry BVol. 128(45)
University of Hawaiʻi at Mānoa (US), Centre National de la Recherche Scientifique (FR), University of Illinois Urbana-Champaign (US), Medical College of Wisconsin (US), Université Paris Cité (FR), Temple College (US), University of Chicago (US), Laboratoire de Biochimie Théorique (FR), Institute of Biophysics and Biomedical Engineering (BG), National Heart, Lung, and Blood Institute (US), Institut de Biologie Physico-Chimique (FR), National Institute of Neurological Disorders and Stroke (US), Institute of Theoretical Physics (CN), Institute of Biophysics (BG), Laboratoire de Physique et Chimie Théoriques, Temple University (US), Université de Lorraine (FR)
Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Medical College of Wisconsin, Agence Nationale de la Recherche, Centre National de la Recherche Scientifique, National Institutes of Health, University of Illinois at Urbana-Champaign, National Heart, Lung, and Blood Institute, National Institute of General Medical Sciences, National Institute of Neurological Disorders and Stroke, H2020 European Research Council
Openalex Percentile: Top 2%
Protein Structure and Dynamics
7.72
DOIOpen Access PDFOpenAlex
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