@article{Fiorin2013,
Author = {Fiorin, Giacomo and Klein, Michael L. and H\'enin, J\'er\^ome},
Title = {Using collective variables to drive molecular dynamics simulations},
Journal = {Molecular Physics},
Year = {2013},
Volume = {111},
Number = {22-23, SI},
Pages = {3345-3362},
Month = {Dec 1},
Abstract = {A software framework is introduced that facilitates the application of
   biasing algorithms to collective variables of the type commonly employed
   to drive massively parallel molecular dynamics (MD) simulations. The
   modular framework that is presented enables one to combine existing
   collective variables into new ones, and combine any chosen collective
   variable with available biasing methods. The latter include the classic
   time-dependent biases referred to as steered MD and targeted MD, the
   temperature-accelerated MD algorithm, as well as the adaptive
   free-energy biases called metadynamics and adaptive biasing force. The
   present modular software is extensible, and portable between commonly
   used MD simulation engines.},
Publisher = {Taylor \& Francis Ltd},
Address = {4 Park Square, Milton Park, Abingdon OX14 4RN, Oxon, England},
Type = {Article},
Language = {English},
Affiliation = {Fiorin, G (Reprint Author), Temple Univ, Dept Chem, Philadelphia, PA 19122 USA.
   Fiorin, Giacomo; Klein, Michael L., Temple Univ, Dept Chem, Philadelphia, PA 19122 USA.
   Fiorin, Giacomo; Klein, Michael L., Temple Univ, Inst Computat Mol Sci, Philadelphia, PA 19122 USA.
   Henin, Jerome, CNRS, Inst Biol Phys Chim, Lab Biochim Theor, Paris, France.},
DOI = {10.1080/00268976.2013.813594},
ISSN = {0026-8976},
EISSN = {1362-3028},
Keywords = {molecular dynamics simulation; collective variable; free-energy
   calculation; adaptive bias; sampling},
Keywords-Plus = {Free-Energy Calculations; Replica-Exchange Method; Force-Field; Reaction
   Coordinate; Orthogonal Space; Efficient; Proteins; Quaternions; Systems;
   Complex},
Research-Areas = {Physics},
Web-of-Science-Categories  = {Physics, Atomic, Molecular \& Chemical},
Author-Email = {giacomo.fiorin@temple.edu},
ResearcherID-Numbers = {Henin, Jerome/A-7080-2008},
ORCID-Numbers = {Henin, Jerome/0000-0003-2540-4098},
Funding-Acknowledgement = {NSF {[}CHE-1212416]; NSF-XSEDE {[}TG-MCA93S020]; GENCI-CINES
   {[}2012-076198]},
Funding-Text = {The authors thank Klaus Schulten and James Phillips for their help in
   extending NAMD, and Christopher Harrison and Christophe Chipot for many
   constructive discussions. Axel Kohlmeyer is gratefully acknowledged for
   linking the software with LAMMPS, and Li Li for contributing the
   well-tempered metadynamics feature. Finally, we are indebted to the
   hundreds of users of the colvars module, whose feedback continues to be
   instrumental to the functionality and robustness of the software since
   its initial release. Part of this work was supported by NSF grant
   CHE-1212416. Access to supercomputing resources was provided by the
   NSF-XSEDE program (allocation TG-MCA93S020) and the GENCI-CINES program
   (grant number 2012-076198).},
Journal-ISO = {Mol. Phys.},
Doc-Delivery-Number = {256GB},
Unique-ID = {ISI:000327296600006},
}