
% GROMACS engine
@article{Abraham2015,
  title = {{GROMACS}: High performance molecular simulations through multi-level parallelism from laptops to supercomputers},
  author = {Abraham, Mark J.{} and Murtola, Teemu and Schulz, Roland and Páll, Szil\'ard and Smith, Jeremy C.{} and Hess, Berk and Lindahl, Erik},
  journal = {{SoftwareX}},
  volume = {1--2},
  year = {2015},
  pages = {19--25},
  doi = {10.1016/j.softx.2015.06.001},
  url = {https://doi.org/10.1016/j.softx.2015.06.001}
}

% BAOA integrator
@article{BouRabee2010,
  doi = {10.1137/090758842},
  url = {https://doi.org/10.1137/090758842},
  year = {2010},
  volume = {48},
  number = {1},
  pages = {278--297},
  author = {Nawaf Bou-Rabee and Houman Owhadi},
  title = {Long-Run Accuracy of Variational Integrators in the Stochastic Context},
  journal = {{SIAM} Journal on Numerical Analysis}
}

% reweightaMD colvar bias implementation (NAMD)
@article{Chen2021,
  author = {Chen, Haochuan and Fu, Haohao and Chipot, Christophe and Shao, Xueguang and Cai, Wensheng},
  title = {Overcoming free-energy barriers with a seamless combination of a biasing force and a collective variable-independent boost potential},
  journal = {J. Chem. Theory Comput.},
  year = {2021},
  volume = {17},
  number = {7},
  pages = {3886--3894},
  doi = {10.1021/acs.jctc.1c00103},
  url = {https://doi.org/10.1021/acs.jctc.1c00103}
}

% neuralNetwork colvar component
@article{Chen2022,
  author = {Chen, Haochuan and Liu, Han and Feng, Heying and Fu, Haohao and Cai, Wensheng and Shao, Xueguang and Chipot, Christophe},
  title = {MLCV: {Bridging} {Machine-Learning-Based} {Dimensionality} {Reduction} and {Free-Energy} {Calculation}},
  journal = {J. Chem. Inf. Model.},
  volume = {62},
  number = {1},
  pages = {1-8},
  year = {2022},
  doi = {10.1021/acs.jcim.1c01010},
  URL = {https://doi.org/10.1021/acs.jcim.1c01010}
}

% Multiple-walker ABF implementation
@article{Comer2014c,
  author = {Comer, Jeffrey and Phillips, James C.{} and Schulten, Klaus and Chipot, Christophe},
  title = {Multiple-walker strategies for free-energy calculations in {NAMD}: {Shared} adaptive biasing force and walker selection rules},
  journal = {J. Chem. Theor. Comput.},
  year = {2014},
  volume = {10},
  number = {12},
  pages = {5276--5285},
  doi = {10.1021/ct500874p},
  pmid = {26583211},
  url = {https://doi.org/10.1021/ct500874p}
}

% Symmetry-adapted RMSD
@article {Ebrahimi2022,
  author = {Ebrahimi, Mina and H\'enin, J\'er\^ome},
  title = {Symmetry-Adapted Restraints for Binding Free Energy Calculations},
  journal = {Journal of Chemical Theory and Computation},
  volume = {18},
  number = {4},
  pages = {2494-2502},
  year = {2022},
  doi = {10.1021/acs.jctc.1c01235},
  url = {https://doi.org/10.1021/acs.jctc.1c01235}
}

% Colvars module
% Colvars-NAMD interface
% Colvars-LAMMPS interface
% Colvars-VMD interface (command line)
% distance colvar component
% distanceXY colvar component (derived from distanceZ)
% distanceZ colvar component
% distanceVec colvar component (derived from distance)
% distanceDir colvar component (derived from distance)
% distanceInv colvar component
% angle colvar component
% dihedral colvar component
% coordNum colvar component
% selfCoordNum colvar component
% groupCoord colvar component (derived from distance)
% hBond colvar component
% rmsd colvar component
% eigenvector colvar component
% gyration colvar component
% inertia colvar component (derived from gyration)
% inertiaZ colvar component (derived from inertia)
% orientation colvar component
% Moving frame of reference
% Optimal rotation via flexible fitting
% orientationAngle colvar component (derived from orientation)
% orientationProj colvar component (derived from orientationAngle)
% spinAngle colvar component (derived from tilt)
% tilt colvar component (derived from orientationProj)
% alpha colvar component
% dihedralPC colvar component
% cartesian colvar component
% Linear and polynomial combination of colvar components
% Metadynamics colvar bias implementation
% Multiple-walker metadynamics colvar bias implementation
% Harmonic colvar bias implementation
% harmonicWalls colvar bias implementation
% Linear colvar bias implementation
% Histogram colvar bias implementation
@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 = {Mol. Phys.},
  year = {2013},
  volume = {111},
  number = {22-23},
  pages = {3345--3362},
  publisher = {Taylor & Francis},
  doi = {10.1080/00268976.2013.813594},
  url = {https://doi.org/10.1080/00268976.2013.813594}
}

% mapTotal colvar component
% Volumetric map-based collective variables
% Multi-Map collective variables
@article{Fiorin2020,
  author = {Fiorin, Giacomo and Marinelli, Fabrizio and {Faraldo-G\'omez}, Jos\'e D.},
  title = {Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics},
  journal = {J. Comp. Chem.},
  year = {2020},
  volume = {41},
  number = {5},
  pages = {449--459},
  doi = {10.1002/jcc.26075},
  pmid = {31602694},
  url = {https://doi.org/10.1002/jcc.26075}
}

% Colvars-GROMACS interface
% gspath colvar component
% gzpath colvar component
% linearCombination colvar component
% gspathCV colvar component
% gzpathCV colvar component
% aspathCV colvar component
% azpathCV colvar component
% Custom functions (Lepton)
% Scripted functions (Tcl)
% ABMD bias
% Updated multiple-walker ABF implementation
@article{Fiorin2024,
  author = {Fiorin, Giacomo and Marinelli, Fabrizio and Forrest, Lucy R. and Chen, Haochuan and Chipot, Christophe and Kohlmeyer, Axel and Santuz, Hubert and H{\'e}nin, J{\'e}rôme},
  title = {Expanded Functionality and Portability for the Colvars Library},
  journal = {J. Phys. Chem. {B}},
  volume = {128},
  number = {45},
  pages = {11108--11123},
  year = {2024},
  doi = {10.1021/acs.jpcb.4c05604},
  pmid = 39501453,
  url = { https://doi.org/10.1021/acs.jpcb.4c05604}
}

% Umbrella-integration eABF estimator
@article{Fu2016,
  author = {Fu, Haohao and Shao, Xueguang and Chipot, Christophe and Cai, Wensheng},
  title = {Extended adaptive biasing force algorithm. {An} on--the--fly implementation for accurate free--energy calculations},
  journal = {J. Chem. Theory Comput.},
  year = {2016},
  volume = {12},
  number = {8},
  pages = {3506-–3513},
  pmid = {27398726},
  doi = {10.1021/acs.jctc.6b00447},
  pmid = {27398726},
  url = {https://doi.org/10.1021/acs.jctc.6b00447}
}

% polarTheta colvar component
% polarPhi colvar component
% eulerPhi colvar component (derived from orientation_angle)
% eulerTheta colvar component (derived from orientation_angle)
% eulerPsi colvar component (derived from orientation_angle)
@article{Fu2017,
  author = {Fu, Haohao and Cai, Wensheng and H\'enin, J\'er\^ome and Roux, Beno\^it and Chipot, Christophe},
  title = {New Coarse Variables for the Accurate Determination of Standard Binding Free Energies},
  journal = {J. Chem. Theory. Comput.},
  year = {2017},
  volume = {13},
  number = {11},
  pages = {5173-5178},
  doi = {10.1021/acs.jctc.7b00791},
  pmid = {28965398},
  url = {https://doi.org/10.1021/acs.jctc.7b00791}
}

% dipoleAngle colvar component
% dipoleMagnitude colvar component
@article{Garate2019,
  author = {Garate, Jos\'e Antonio and Bernardin, Alejandro and Escalona, Yerko and Yanez, Carlos and English, Niall J.{} and {Perez-Acle}, Tomas},
  title = {Orientational and Folding Thermodynamics via Electric Dipole Moment Restraining},
  journal = {J. Phys. Chem. {B}},
  year = {2019},
  volume = {123},
  number = {12},
  pages = {2599--2608},
  doi = {10.1021/acs.jpcb.8b09374},
  pmid = {30831028},
  url = {https://doi.org/10.1021/acs.jpcb.8b09374}
}

% ABF colvar bias implementation
% Internal-forces free energy estimator
@article{Henin2010,
  author = {H\'enin, J\'er\^ome and Fiorin, Giacomo and Chipot, Christophe and Klein, Michael L.},
  title = {Exploring multidimensional free energy landscapes using time-dependent biases on collective variables},
  journal = {J. Chem. Theory Comput.},
  year = {2010},
  volume = {6},
  pages = {35-47},
  number = {1},
  doi = {10.1021/ct9004432},
  pmid = {26614317},
  url = {https://doi.org/10.1021/ct9004432}
}

% Poisson integration of 2D/3D free energy surfaces
@Article{Henin2021,
  author  = {H\'enin, J.},
  journal = {J. Chem. Theory Comput.},
  title   = {Fast and accurate multidimensional free energy integration},
  year    = {2021},
  doi     = {10.1021/acs.jctc.1c00593},
  url     = {https://doi.org/10.1021/acs.jctc.1c00593},
}

% VMD engine
@article{Humphrey1996,
  title = {{VMD}: visual molecular dynamics},
  author = {Humphrey, William and Dalke, Andrew and Schulten, Klaus},
  journal = {J. Mol. Graph.},
  year = {1996},
  volume = {14},
  number = {1},
  pages = {33--38},
  doi = {10.1016/0263-7855(96)00018-5},
  url = {https://doi.org/10.1016/0263-7855(96)00018-5}
}

% alchLambda colvar component
% alchFLambda colvar component
% Tinker-HP interface
@misc{Lagardere2023,
      title={Lambda-ABF: Simplified, Accurate and Cost-effective Alchemical Free Energy Computations},
      author={Louis Lagard\`ere and Lise Maurin and Olivier Adjoua and Krystel El Hage and Pierre Monmarch\'e and Jean-Philip Piquemal and J\'er\^ome H\'enin},
      year={2023},
      eprint={2307.08006},
      archivePrefix={arXiv},
      primaryClass={physics.chem-ph},
      url = {https://arxiv.org/abs/2307.08006}
}

% eABF implementation
% CZAR eABF estimator
@article{Lesage2017,
  author = {Lesage, Adrien and Leli\`evre, Tony and Stoltz, Gabriel and H\'enin, J\'er\^ome},
  title = {Smoothed biasing forces yield unbiased free energies with the extended-system adaptive biasing force method},
  journal = {J. Phys. Chem. {B}},
  year = {2017},
  volume = {121},
  number = {15},
  pages = {3676-3685},
  doi = {10.1021/acs.jpcb.6b10055},
  pmid = {27959559},
  url = {https://doi.org/10.1021/acs.jpcb.6b10055}
}

% Ensemble-biased metadynamics (ebMetaD)
@article{Marinelli2015,
  author = {Marinelli, Fabrizio and Faraldo-G\'omez, Jos\'e D.},
  title = {Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions},
  journal = {Biophys. J.},
  year = {2015},
  volume = {108},
  number = {12},
  pages = {2779--2782},
  doi = {10.1016/j.bpj.2015.05.024},
  pmid = {26083917},
  url = {https://doi.org/10.1016/j.bpj.2015.05.024}
}

% NAMD engine
% Scalable center-of-mass computation (NAMD)
@article{Phillips2020,
  author = {Phillips, James C.{} and Hardy, David J.{} and Maia, Julio D. C.{} and Stone, John E.{} and Ribeiro, Jo\~ao V.{} and Bernardi, Rafael C.{} and Buch, Ronak and Fiorin, Giacomo and H\'enin, J\'er\^ome and Jiang, Wei and McGreevy, Ryan and Melo, Marcelo C. R.{} and Radak, Brian K.{} and Skeel, Robert D.{} and Singharoy, Abhishek and Wang, Yi and Roux, Beno\^it and Aksimentiev, Aleksei and Luthey-Schulten, Zaida and Kal\'e, Laxmikant V.{} and Schulten, Klaus and Chipot, Christophe and Tajkhorshid, Emad},
  title = {Scalable molecular dynamics on {CPU} and {GPU} architectures with {NAMD}},
  journal = {J. Chem. Phys.},
  year = {2020},
  volume = {153},
  number = {4},
  pages = {044130},
  doi = {10.1063/5.0014475},
  pmid = {32752662},
  url = {https://doi.org/10.1063/5.0014475}
}

% LAMMPS engine
@article{Thompson2022,
  title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
  author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
  journal = {Comp. Phys. Comm.},
  volume = {271},
  pages = {108171},
  year = {2022},
  doi = {10.1016/j.cpc.2021.108171},
  url = {https://doi.org/10.1016/j.cpc.2021.108171}
}

% distancePairs colvar component
% histogramRestraint colvar bias implementation
@article{Shen2015,
  title = {Structural refinement of proteins by restrained molecular dynamics simulations with non-interacting molecular fragments},
  author = {Shen, Rong and Han, Wei and Fiorin, Giacomo and Islam, Shahidul M and Schulten, Klaus and Roux, Beno{\^\i}t},
  journal = {{PLoS} Comput. Biol.},
  volume = {11},
  year = {2015},
  number = {10},
  pages = {e1004368},
  doi = {10.1371/journal.pcbi.1004368},
  pmid = {26505197},
  url = {https://doi.org/10.1371/journal.pcbi.1004368}
}

% GridForces volumetric map implementation for NAMD
@article{Wells2007,
  author = {Wells, David B. and Abramkina, Volha and Aksimentiev, Aleksei},
  title = {Exploring transmembrane transport through $\alpha$-hemolysin with grid-steered molecular dynamics},
  journal = {J. Chem. Phys.},
  year = {2007},
  volume = {127},
  number = {12},
  pages = {125101},
  doi = {10.1063/1.2770738},
  pmid = {17902937},
  url = {https://doi.org/10.1063/1.2770738}
}

% ALB colvar bias implementation
@article{White2014,
  author = {White, Andrew D.{} and Voth, Gregory A.{}},
  title = {Efficient and minimal method to bias molecular simulations with experimental data},
  journal = {J. Chem. Theory Comput.},
  year = {2014},
  volume = {10},
  number = {8},
  pages = {3023-–3030},
  doi = {10.1021/ct500320c},
  pmid = {26588273},
  url = {https://doi.org/10.1021/ct500320c}
}

% OPES
@article{Invernizzi2020,
	title = {Rethinking {Metadynamics}: {From} {Bias} {Potentials} to {Probability} {Distributions}},
	volume = {11},
	issn = {1948-7185, 1948-7185},
	shorttitle = {Rethinking {Metadynamics}},
	url = {https://pubs.acs.org/doi/10.1021/acs.jpclett.0c00497},
	doi = {10.1021/acs.jpclett.0c00497},
	number = {7},
	urldate = {2020-09-30},
	journal = {J. Phys. Chem. Lett.},
	author = {Invernizzi, Michele and Parrinello, Michele},
	month = apr,
	year = {2020},
	pages = {2731--2736},
}

% OPES explore or adaptive kernels
@article{Invernizzi2022,
	title = {Exploration vs {Convergence} {Speed} in {Adaptive}-{Bias} {Enhanced} {Sampling}},
	volume = {18},
	issn = {1549-9618},
	url = {https://doi.org/10.1021/acs.jctc.2c00152},
	doi = {10.1021/acs.jctc.2c00152},
	number = {6},
	urldate = {2024-07-02},
	journal = {J. Chem. Theory Comput.},
	author = {Invernizzi, Michele and Parrinello, Michele},
	month = jun,
	year = {2022},
	pages = {3988--3996},
}

% --- NO CITATIONS AVAILABLE YET FOR THESE FEATURES ---
% coordNum pairlist
% torchANN colvar component
% --- END ---
