00001
00002 paper_count_[std::string("Abraham2015")] = 0;
00003 paper_url_[std::string("Abraham2015")] = "https://doi.org/10.1016/j.softx.2015.06.001";
00004 paper_bibtex_[std::string("Abraham2015")] =
00005 "\n"
00006 "@article{Abraham2015,\n"
00007 " title = {{GROMACS}: High performance molecular simulations through multi-level parallelism from laptops to supercomputers},\n"
00008 " author = {Abraham, Mark J.{} and Murtola, Teemu and Schulz, Roland and Páll, Szil\\'ard and Smith, Jeremy C.{} and Hess, Berk and Lindahl, Erik},\n"
00009 " journal = {{SoftwareX}},\n"
00010 " volume = {1--2},\n"
00011 " year = {2015},\n"
00012 " pages = {19--25},\n"
00013 " doi = {10.1016/j.softx.2015.06.001},\n"
00014 " url = {https://doi.org/10.1016/j.softx.2015.06.001}\n"
00015 "}\n";
00016
00017 paper_count_[std::string("Chen2021")] = 0;
00018 paper_url_[std::string("Chen2021")] = "https://doi.org/10.1021/acs.jctc.1c00103";
00019 paper_bibtex_[std::string("Chen2021")] =
00020 "\n"
00021 "@article{Chen2021,\n"
00022 " author = {Chen, Haochuan and Fu, Haohao and Chipot, Christophe and Shao, Xueguang and Cai, Wensheng},\n"
00023 " title = {Overcoming free-energy barriers with a seamless combination of a biasing force and a collective variable-independent boost potential},\n"
00024 " journal = {J. Chem. Theory Comput.},\n"
00025 " year = {2021},\n"
00026 " volume = {17},\n"
00027 " number = {7},\n"
00028 " pages = {3886--3894},\n"
00029 " doi = {10.1021/acs.jctc.1c00103},\n"
00030 " url = {https://doi.org/10.1021/acs.jctc.1c00103}\n"
00031 "}\n";
00032
00033 paper_count_[std::string("Chen2022")] = 0;
00034 paper_url_[std::string("Chen2022")] = "https://doi.org/10.1021/acs.jcim.1c01010";
00035 paper_bibtex_[std::string("Chen2022")] =
00036 "\n"
00037 "@article{Chen2022,\n"
00038 " author = {Chen, Haochuan and Liu, Han and Feng, Heying and Fu, Haohao and Cai, Wensheng and Shao, Xueguang and Chipot, Christophe},\n"
00039 " title = {MLCV: {Bridging} {Machine-Learning-Based} {Dimensionality} {Reduction} and {Free-Energy} {Calculation}},\n"
00040 " journal = {J. Chem. Inf. Model.},\n"
00041 " volume = {62},\n"
00042 " number = {1},\n"
00043 " pages = {1-8},\n"
00044 " year = {2022},\n"
00045 " doi = {10.1021/acs.jcim.1c01010},\n"
00046 " URL = {https://doi.org/10.1021/acs.jcim.1c01010}\n"
00047 "}\n";
00048
00049 paper_count_[std::string("Comer2014c")] = 0;
00050 paper_url_[std::string("Comer2014c")] = "https://doi.org/10.1021/ct500874p";
00051 paper_bibtex_[std::string("Comer2014c")] =
00052 "\n"
00053 "@article{Comer2014c,\n"
00054 " author = {Comer, Jeffrey and Phillips, James C.{} and Schulten, Klaus and Chipot, Christophe},\n"
00055 " title = {Multiple-walker strategies for free-energy calculations in {NAMD}: {Shared} adaptive biasing force and walker selection rules},\n"
00056 " journal = {J. Chem. Theor. Comput.},\n"
00057 " year = {2014},\n"
00058 " volume = {10},\n"
00059 " number = {12},\n"
00060 " pages = {5276--5285},\n"
00061 " doi = {10.1021/ct500874p},\n"
00062 " pmid = {26583211},\n"
00063 " url = {https://doi.org/10.1021/ct500874p}\n"
00064 "}\n";
00065
00066 paper_count_[std::string("Ebrahimi2022")] = 0;
00067 paper_url_[std::string("Ebrahimi2022")] = "https://doi.org/10.1021/acs.jctc.1c01235";
00068 paper_bibtex_[std::string("Ebrahimi2022")] =
00069 "\n"
00070 "@article {Ebrahimi2022,\n"
00071 " author = {Ebrahimi, Mina and H\\'enin, J\\'er\\^ome},\n"
00072 " title = {Symmetry-Adapted Restraints for Binding Free Energy Calculations},\n"
00073 " journal = {Journal of Chemical Theory and Computation},\n"
00074 " volume = {18},\n"
00075 " number = {4},\n"
00076 " pages = {2494-2502},\n"
00077 " year = {2022},\n"
00078 " doi = {10.1021/acs.jctc.1c01235},\n"
00079 " url = {https://doi.org/10.1021/acs.jctc.1c01235}\n"
00080 "}\n";
00081
00082 paper_count_[std::string("Fiorin2013")] = 0;
00083 paper_url_[std::string("Fiorin2013")] = "https://doi.org/10.1080/00268976.2013.813594";
00084 paper_bibtex_[std::string("Fiorin2013")] =
00085 "\n"
00086 "@article{Fiorin2013,\n"
00087 " author = {Fiorin, Giacomo and Klein, Michael L.{} and H\\'enin, J\\'er\\^ome},\n"
00088 " title = {Using collective variables to drive molecular dynamics simulations},\n"
00089 " journal = {Mol. Phys.},\n"
00090 " year = {2013},\n"
00091 " volume = {111},\n"
00092 " number = {22-23},\n"
00093 " pages = {3345--3362},\n"
00094 " publisher = {Taylor & Francis},\n"
00095 " doi = {10.1080/00268976.2013.813594},\n"
00096 " url = {https://doi.org/10.1080/00268976.2013.813594}\n"
00097 "}\n";
00098
00099 paper_count_[std::string("Fiorin2020")] = 0;
00100 paper_url_[std::string("Fiorin2020")] = "https://doi.org/10.1002/jcc.26075";
00101 paper_bibtex_[std::string("Fiorin2020")] =
00102 "\n"
00103 "@article{Fiorin2020,\n"
00104 " author = {Fiorin, Giacomo and Marinelli, Fabrizio and {Faraldo-G\\'omez}, Jos\\'e D.},\n"
00105 " title = {Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics},\n"
00106 " journal = {J. Comp. Chem.},\n"
00107 " year = {2020},\n"
00108 " volume = {41},\n"
00109 " number = {5},\n"
00110 " pages = {449--459},\n"
00111 " doi = {10.1002/jcc.26075},\n"
00112 " pmid = {31602694},\n"
00113 " url = {https://doi.org/10.1002/jcc.26075}\n"
00114 "}\n";
00115
00116 paper_count_[std::string("Fu2016")] = 0;
00117 paper_url_[std::string("Fu2016")] = "https://doi.org/10.1021/acs.jctc.6b00447";
00118 paper_bibtex_[std::string("Fu2016")] =
00119 "\n"
00120 "@article{Fu2016,\n"
00121 " author = {Fu, Haohao and Shao, Xueguang and Chipot, Christophe and Cai, Wensheng},\n"
00122 " title = {Extended adaptive biasing force algorithm. {An} on--the--fly implementation for accurate free--energy calculations},\n"
00123 " journal = {J. Chem. Theory Comput.},\n"
00124 " year = {2016},\n"
00125 " volume = {12},\n"
00126 " number = {8},\n"
00127 " pages = {3506-–3513},\n"
00128 " pmid = {27398726},\n"
00129 " doi = {10.1021/acs.jctc.6b00447},\n"
00130 " pmid = {27398726},\n"
00131 " url = {https://doi.org/10.1021/acs.jctc.6b00447}\n"
00132 "}\n";
00133
00134 paper_count_[std::string("Fu2017")] = 0;
00135 paper_url_[std::string("Fu2017")] = "https://doi.org/10.1021/acs.jctc.7b00791";
00136 paper_bibtex_[std::string("Fu2017")] =
00137 "\n"
00138 "@article{Fu2017,\n"
00139 " author = {Fu, Haohao and Cai, Wensheng and H\\'enin, J\\'er\\^ome and Roux, Beno\\^it and Chipot, Christophe},\n"
00140 " title = {New Coarse Variables for the Accurate Determination of Standard Binding Free Energies},\n"
00141 " journal = {J. Chem. Theory. Comput.},\n"
00142 " year = {2017},\n"
00143 " volume = {13},\n"
00144 " number = {11},\n"
00145 " pages = {5173-5178},\n"
00146 " doi = {10.1021/acs.jctc.7b00791},\n"
00147 " pmid = {28965398},\n"
00148 " url = {https://doi.org/10.1021/acs.jctc.7b00791}\n"
00149 "}\n";
00150
00151 paper_count_[std::string("Garate2019")] = 0;
00152 paper_url_[std::string("Garate2019")] = "https://doi.org/10.1021/acs.jpcb.8b09374";
00153 paper_bibtex_[std::string("Garate2019")] =
00154 "\n"
00155 "@article{Garate2019,\n"
00156 " author = {Garate, Jos\\'e Antonio and Bernardin, Alejandro and Escalona, Yerko and Yanez, Carlos and English, Niall J.{} and {Perez-Acle}, Tomas},\n"
00157 " title = {Orientational and Folding Thermodynamics via Electric Dipole Moment Restraining},\n"
00158 " journal = {J. Phys. Chem. {B}},\n"
00159 " year = {2019},\n"
00160 " volume = {123},\n"
00161 " number = {12},\n"
00162 " pages = {2599--2608},\n"
00163 " doi = {10.1021/acs.jpcb.8b09374},\n"
00164 " pmid = {30831028},\n"
00165 " url = {https://doi.org/10.1021/acs.jpcb.8b09374}\n"
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00167
00168 paper_count_[std::string("Henin2010")] = 0;
00169 paper_url_[std::string("Henin2010")] = "https://doi.org/10.1021/ct9004432";
00170 paper_bibtex_[std::string("Henin2010")] =
00171 "\n"
00172 "@article{Henin2010,\n"
00173 " author = {H\\'enin, J\\'er\\^ome and Fiorin, Giacomo and Chipot, Christophe and Klein, Michael L.},\n"
00174 " title = {Exploring multidimensional free energy landscapes using time-dependent biases on collective variables},\n"
00175 " journal = {J. Chem. Theory Comput.},\n"
00176 " year = {2010},\n"
00177 " volume = {6},\n"
00178 " pages = {35-47},\n"
00179 " number = {1},\n"
00180 " doi = {10.1021/ct9004432},\n"
00181 " pmid = {26614317},\n"
00182 " url = {https://doi.org/10.1021/ct9004432}\n"
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00185 paper_count_[std::string("Humphrey1996")] = 0;
00186 paper_url_[std::string("Humphrey1996")] = "https://doi.org/10.1016/0263-7855(96)00018-5";
00187 paper_bibtex_[std::string("Humphrey1996")] =
00188 "\n"
00189 "@article{Humphrey1996,\n"
00190 " title = {{VMD}: visual molecular dynamics},\n"
00191 " author = {Humphrey, William and Dalke, Andrew and Schulten, Klaus},\n"
00192 " journal = {J. Mol. Graph.},\n"
00193 " year = {1996},\n"
00194 " volume = {14},\n"
00195 " number = {1},\n"
00196 " pages = {33--38},\n"
00197 " doi = {10.1016/0263-7855(96)00018-5},\n"
00198 " url = {https://doi.org/10.1016/0263-7855(96)00018-5}\n"
00199 "}\n";
00200
00201 paper_count_[std::string("Lesage2017")] = 0;
00202 paper_url_[std::string("Lesage2017")] = "https://doi.org/10.1021/acs.jpcb.6b10055";
00203 paper_bibtex_[std::string("Lesage2017")] =
00204 "\n"
00205 "@article{Lesage2017,\n"
00206 " author = {Lesage, Adrien and Leli\\`evre, Tony and Stoltz, Gabriel and H\\'enin, J\\'er\\^ome},\n"
00207 " title = {Smoothed biasing forces yield unbiased free energies with the extended-system adaptive biasing force method},\n"
00208 " journal = {J. Phys. Chem. {B}},\n"
00209 " year = {2017},\n"
00210 " volume = {121},\n"
00211 " number = {15},\n"
00212 " pages = {3676-3685},\n"
00213 " doi = {10.1021/acs.jpcb.6b10055},\n"
00214 " pmid = {27959559},\n"
00215 " url = {https://doi.org/10.1021/acs.jpcb.6b10055}\n"
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00217
00218 paper_count_[std::string("Henin2021")] = 0;
00219 paper_url_[std::string("Henin2021")] = "https://doi.org/10.1021/acs.jctc.1c00593";
00220 paper_bibtex_[std::string("Henin2021")] =
00221 "\n"
00222 "@Article{Henin2021,\n"
00223 " author = {H\\'enin, J.},\n"
00224 " journal = {J. Chem. Theory Comput.},\n"
00225 " title = {Fast and accurate multidimensional free energy integration},\n"
00226 " year = {2021},\n"
00227 " doi = {10.1021/acs.jctc.1c00593},\n"
00228 " url = {https://doi.org/10.1021/acs.jctc.1c00593},\n"
00229 "}\n";
00230
00231 paper_count_[std::string("Marinelli2015")] = 0;
00232 paper_url_[std::string("Marinelli2015")] = "https://doi.org/10.1016/j.bpj.2015.05.024";
00233 paper_bibtex_[std::string("Marinelli2015")] =
00234 "\n"
00235 "@article{Marinelli2015,\n"
00236 " author = {Marinelli, Fabrizio and Faraldo-G\\'omez, Jos\\'e D.},\n"
00237 " title = {Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions},\n"
00238 " journal = {Biophys. J.},\n"
00239 " year = {2015},\n"
00240 " volume = {108},\n"
00241 " number = {12},\n"
00242 " pages = {2779--2782},\n"
00243 " doi = {10.1016/j.bpj.2015.05.024},\n"
00244 " pmid = {26083917},\n"
00245 " url = {https://doi.org/10.1016/j.bpj.2015.05.024}\n"
00246 "}\n";
00247
00248 paper_count_[std::string("Phillips2020")] = 0;
00249 paper_url_[std::string("Phillips2020")] = "https://doi.org/10.1063/5.0014475";
00250 paper_bibtex_[std::string("Phillips2020")] =
00251 "\n"
00252 "@article{Phillips2020,\n"
00253 " 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},\n"
00254 " title = {Scalable molecular dynamics on {CPU} and {GPU} architectures with {NAMD}},\n"
00255 " journal = {J. Chem. Phys.},\n"
00256 " year = {2020},\n"
00257 " volume = {153},\n"
00258 " number = {4},\n"
00259 " pages = {044130},\n"
00260 " doi = {10.1063/5.0014475},\n"
00261 " pmid = {32752662},\n"
00262 " url = {https://doi.org/10.1063/5.0014475}\n"
00263 "}\n";
00264
00265 paper_count_[std::string("Thompson2022")] = 0;
00266 paper_url_[std::string("Thompson2022")] = "https://doi.org/10.1016/j.cpc.2021.108171";
00267 paper_bibtex_[std::string("Thompson2022")] =
00268 "\n"
00269 "@article{Thompson2022,\n"
00270 " title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},\n"
00271 " 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.},\n"
00272 " journal = {Comp. Phys. Comm.},\n"
00273 " volume = {271},\n"
00274 " pages = {108171},\n"
00275 " year = {2022},\n"
00276 " doi = {10.1016/j.cpc.2021.108171},\n"
00277 " url = {https://doi.org/10.1016/j.cpc.2021.108171}\n"
00278 "}\n";
00279
00280 paper_count_[std::string("Shen2015")] = 0;
00281 paper_url_[std::string("Shen2015")] = "https://doi.org/10.1371/journal.pcbi.1004368";
00282 paper_bibtex_[std::string("Shen2015")] =
00283 "\n"
00284 "@article{Shen2015,\n"
00285 " title = {Structural refinement of proteins by restrained molecular dynamics simulations with non-interacting molecular fragments},\n"
00286 " author = {Shen, Rong and Han, Wei and Fiorin, Giacomo and Islam, Shahidul M and Schulten, Klaus and Roux, Beno{\\^\\i}t},\n"
00287 " journal = {{PLoS} Comput. Biol.},\n"
00288 " volume = {11},\n"
00289 " year = {2015},\n"
00290 " number = {10},\n"
00291 " pages = {e1004368},\n"
00292 " doi = {10.1371/journal.pcbi.1004368},\n"
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00294 " url = {https://doi.org/10.1371/journal.pcbi.1004368}\n"
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00296
00297 paper_count_[std::string("Wells2007")] = 0;
00298 paper_url_[std::string("Wells2007")] = "https://doi.org/10.1063/1.2770738";
00299 paper_bibtex_[std::string("Wells2007")] =
00300 "\n"
00301 "@article{Wells2007,\n"
00302 " author = {Wells, David B. and Abramkina, Volha and Aksimentiev, Aleksei},\n"
00303 " title = {Exploring transmembrane transport through $\\alpha$-hemolysin with grid-steered molecular dynamics},\n"
00304 " journal = {J. Chem. Phys.},\n"
00305 " year = {2007},\n"
00306 " volume = {127},\n"
00307 " number = {12},\n"
00308 " pages = {125101},\n"
00309 " doi = {10.1063/1.2770738},\n"
00310 " pmid = {17902937},\n"
00311 " url = {https://doi.org/10.1063/1.2770738}\n"
00312 "}\n";
00313
00314 paper_count_[std::string("White2014")] = 0;
00315 paper_url_[std::string("White2014")] = "https://doi.org/10.1021/ct500320c";
00316 paper_bibtex_[std::string("White2014")] =
00317 "\n"
00318 "@article{White2014,\n"
00319 " author = {White, Andrew D.{} and Voth, Gregory A.{}},\n"
00320 " title = {Efficient and minimal method to bias molecular simulations with experimental data},\n"
00321 " journal = {J. Chem. Theory Comput.},\n"
00322 " year = {2014},\n"
00323 " volume = {10},\n"
00324 " number = {8},\n"
00325 " pages = {3023-–3030},\n"
00326 " doi = {10.1021/ct500320c},\n"
00327 " pmid = {26588273},\n"
00328 " url = {https://doi.org/10.1021/ct500320c}\n"
00329 "}\n";
00330
00331 paper_count_[std::string("n/a")] = 0;
00332 paper_url_[std::string("n/a")] = "";
00333 paper_bibtex_[std::string("n/a")] = "";
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00335 feature_count_[std::string("GROMACS engine")] = 0;
00336 feature_paper_map_[std::string("GROMACS engine")] = "Abraham2015";
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00338 feature_count_[std::string("reweightaMD colvar bias implementation (NAMD)")] = 0;
00339 feature_paper_map_[std::string("reweightaMD colvar bias implementation (NAMD)")] = "Chen2021";
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00342 feature_paper_map_[std::string("neuralNetwork colvar component")] = "Chen2022";
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00345 feature_paper_map_[std::string("Multiple-walker ABF implementation")] = "Comer2014c";
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00348 feature_paper_map_[std::string("Symmetry-adapted RMSD")] = "Ebrahimi2022";
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00350 feature_count_[std::string("Colvars module")] = 0;
00351 feature_paper_map_[std::string("Colvars module")] = "Fiorin2013";
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00353 feature_count_[std::string("Colvars-NAMD interface")] = 0;
00354 feature_paper_map_[std::string("Colvars-NAMD interface")] = "Fiorin2013";
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00356 feature_count_[std::string("Colvars-LAMMPS interface")] = 0;
00357 feature_paper_map_[std::string("Colvars-LAMMPS interface")] = "Fiorin2013";
00358
00359 feature_count_[std::string("Colvars-VMD interface (command line)")] = 0;
00360 feature_paper_map_[std::string("Colvars-VMD interface (command line)")] = "Fiorin2013";
00361
00362 feature_count_[std::string("distance colvar component")] = 0;
00363 feature_paper_map_[std::string("distance colvar component")] = "Fiorin2013";
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00365 feature_count_[std::string("distanceXY colvar component (derived from distanceZ)")] = 0;
00366 feature_paper_map_[std::string("distanceXY colvar component (derived from distanceZ)")] = "Fiorin2013";
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00368 feature_count_[std::string("distanceZ colvar component")] = 0;
00369 feature_paper_map_[std::string("distanceZ colvar component")] = "Fiorin2013";
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00371 feature_count_[std::string("distanceVec colvar component (derived from distance)")] = 0;
00372 feature_paper_map_[std::string("distanceVec colvar component (derived from distance)")] = "Fiorin2013";
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00374 feature_count_[std::string("distanceDir colvar component (derived from distance)")] = 0;
00375 feature_paper_map_[std::string("distanceDir colvar component (derived from distance)")] = "Fiorin2013";
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00377 feature_count_[std::string("distanceInv colvar component")] = 0;
00378 feature_paper_map_[std::string("distanceInv colvar component")] = "Fiorin2013";
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00381 feature_paper_map_[std::string("angle colvar component")] = "Fiorin2013";
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00383 feature_count_[std::string("dihedral colvar component")] = 0;
00384 feature_paper_map_[std::string("dihedral colvar component")] = "Fiorin2013";
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00386 feature_count_[std::string("coordNum colvar component")] = 0;
00387 feature_paper_map_[std::string("coordNum colvar component")] = "Fiorin2013";
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00389 feature_count_[std::string("selfCoordNum colvar component")] = 0;
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00395 feature_count_[std::string("hBond colvar component")] = 0;
00396 feature_paper_map_[std::string("hBond colvar component")] = "Fiorin2013";
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00398 feature_count_[std::string("rmsd colvar component")] = 0;
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00401 feature_count_[std::string("eigenvector colvar component")] = 0;
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00404 feature_count_[std::string("gyration colvar component")] = 0;
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00408 feature_paper_map_[std::string("inertia colvar component (derived from gyration)")] = "Fiorin2013";
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00422 feature_count_[std::string("orientationAngle colvar component (derived from orientation)")] = 0;
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00426 feature_paper_map_[std::string("orientationProj colvar component (derived from orientation)")] = "Fiorin2013";
00427
00428 feature_count_[std::string("spinAngle colvar component (derived from orientation)")] = 0;
00429 feature_paper_map_[std::string("spinAngle colvar component (derived from orientation)")] = "Fiorin2013";
00430
00431 feature_count_[std::string("tilt colvar component (derived from orientation)")] = 0;
00432 feature_paper_map_[std::string("tilt colvar component (derived from orientation)")] = "Fiorin2013";
00433
00434 feature_count_[std::string("alpha colvar component")] = 0;
00435 feature_paper_map_[std::string("alpha colvar component")] = "Fiorin2013";
00436
00437 feature_count_[std::string("dihedralPC colvar component")] = 0;
00438 feature_paper_map_[std::string("dihedralPC colvar component")] = "Fiorin2013";
00439
00440 feature_count_[std::string("cartesian colvar component")] = 0;
00441 feature_paper_map_[std::string("cartesian colvar component")] = "Fiorin2013";
00442
00443 feature_count_[std::string("Linear and polynomial combination of colvar components")] = 0;
00444 feature_paper_map_[std::string("Linear and polynomial combination of colvar components")] = "Fiorin2013";
00445
00446 feature_count_[std::string("Metadynamics colvar bias implementation")] = 0;
00447 feature_paper_map_[std::string("Metadynamics colvar bias implementation")] = "Fiorin2013";
00448
00449 feature_count_[std::string("Multiple-walker metadynamics colvar bias implementation")] = 0;
00450 feature_paper_map_[std::string("Multiple-walker metadynamics colvar bias implementation")] = "Fiorin2013";
00451
00452 feature_count_[std::string("Harmonic colvar bias implementation")] = 0;
00453 feature_paper_map_[std::string("Harmonic colvar bias implementation")] = "Fiorin2013";
00454
00455 feature_count_[std::string("harmonicWalls colvar bias implementation")] = 0;
00456 feature_paper_map_[std::string("harmonicWalls colvar bias implementation")] = "Fiorin2013";
00457
00458 feature_count_[std::string("Linear colvar bias implementation")] = 0;
00459 feature_paper_map_[std::string("Linear colvar bias implementation")] = "Fiorin2013";
00460
00461 feature_count_[std::string("Histogram colvar bias implementation")] = 0;
00462 feature_paper_map_[std::string("Histogram colvar bias implementation")] = "Fiorin2013";
00463
00464 feature_count_[std::string("mapTotal colvar component")] = 0;
00465 feature_paper_map_[std::string("mapTotal colvar component")] = "Fiorin2020";
00466
00467 feature_count_[std::string("Volumetric map-based collective variables")] = 0;
00468 feature_paper_map_[std::string("Volumetric map-based collective variables")] = "Fiorin2020";
00469
00470 feature_count_[std::string("Multi-Map collective variables")] = 0;
00471 feature_paper_map_[std::string("Multi-Map collective variables")] = "Fiorin2020";
00472
00473 feature_count_[std::string("Umbrella-integration eABF estimator")] = 0;
00474 feature_paper_map_[std::string("Umbrella-integration eABF estimator")] = "Fu2016";
00475
00476 feature_count_[std::string("polarTheta colvar component")] = 0;
00477 feature_paper_map_[std::string("polarTheta colvar component")] = "Fu2017";
00478
00479 feature_count_[std::string("polarPhi colvar component")] = 0;
00480 feature_paper_map_[std::string("polarPhi colvar component")] = "Fu2017";
00481
00482 feature_count_[std::string("eulerPhi colvar component (derived from orientation)")] = 0;
00483 feature_paper_map_[std::string("eulerPhi colvar component (derived from orientation)")] = "Fu2017";
00484
00485 feature_count_[std::string("eulerTheta colvar component (derived from orientation)")] = 0;
00486 feature_paper_map_[std::string("eulerTheta colvar component (derived from orientation)")] = "Fu2017";
00487
00488 feature_count_[std::string("eulerPsi colvar component (derived from orientation)")] = 0;
00489 feature_paper_map_[std::string("eulerPsi colvar component (derived from orientation)")] = "Fu2017";
00490
00491 feature_count_[std::string("dipoleAngle colvar component")] = 0;
00492 feature_paper_map_[std::string("dipoleAngle colvar component")] = "Garate2019";
00493
00494 feature_count_[std::string("dipoleMagnitude colvar component")] = 0;
00495 feature_paper_map_[std::string("dipoleMagnitude colvar component")] = "Garate2019";
00496
00497 feature_count_[std::string("ABF colvar bias implementation")] = 0;
00498 feature_paper_map_[std::string("ABF colvar bias implementation")] = "Henin2010";
00499
00500 feature_count_[std::string("Internal-forces free energy estimator")] = 0;
00501 feature_paper_map_[std::string("Internal-forces free energy estimator")] = "Henin2010";
00502
00503 feature_count_[std::string("VMD engine")] = 0;
00504 feature_paper_map_[std::string("VMD engine")] = "Humphrey1996";
00505
00506 feature_count_[std::string("eABF implementation")] = 0;
00507 feature_paper_map_[std::string("eABF implementation")] = "Lesage2017";
00508
00509 feature_count_[std::string("CZAR eABF estimator")] = 0;
00510 feature_paper_map_[std::string("CZAR eABF estimator")] = "Lesage2017";
00511
00512 feature_count_[std::string("Poisson integration of 2D/3D free energy surfaces")] = 0;
00513 feature_paper_map_[std::string("Poisson integration of 2D/3D free energy surfaces")] = "Henin2021";
00514
00515 feature_count_[std::string("Ensemble-biased metadynamics (ebMetaD)")] = 0;
00516 feature_paper_map_[std::string("Ensemble-biased metadynamics (ebMetaD)")] = "Marinelli2015";
00517
00518 feature_count_[std::string("NAMD engine")] = 0;
00519 feature_paper_map_[std::string("NAMD engine")] = "Phillips2020";
00520
00521 feature_count_[std::string("Scalable center-of-mass computation (NAMD)")] = 0;
00522 feature_paper_map_[std::string("Scalable center-of-mass computation (NAMD)")] = "Phillips2020";
00523
00524 feature_count_[std::string("LAMMPS engine")] = 0;
00525 feature_paper_map_[std::string("LAMMPS engine")] = "Thompson2022";
00526
00527 feature_count_[std::string("distancePairs colvar component")] = 0;
00528 feature_paper_map_[std::string("distancePairs colvar component")] = "Shen2015";
00529
00530 feature_count_[std::string("histogramRestraint colvar bias implementation")] = 0;
00531 feature_paper_map_[std::string("histogramRestraint colvar bias implementation")] = "Shen2015";
00532
00533 feature_count_[std::string("GridForces volumetric map implementation for NAMD")] = 0;
00534 feature_paper_map_[std::string("GridForces volumetric map implementation for NAMD")] = "Wells2007";
00535
00536 feature_count_[std::string("ALB colvar bias implementation")] = 0;
00537 feature_paper_map_[std::string("ALB colvar bias implementation")] = "White2014";
00538
00539 feature_count_[std::string("Colvars-GROMACS interface")] = 0;
00540 feature_paper_map_[std::string("Colvars-GROMACS interface")] = "n/a";
00541
00542 feature_count_[std::string("Colvars Dashboard (Colvars-VMD graphical user interface)")] = 0;
00543 feature_paper_map_[std::string("Colvars Dashboard (Colvars-VMD graphical user interface)")] = "n/a";
00544
00545 feature_count_[std::string("gspath colvar component")] = 0;
00546 feature_paper_map_[std::string("gspath colvar component")] = "n/a";
00547
00548 feature_count_[std::string("gzpath colvar component")] = 0;
00549 feature_paper_map_[std::string("gzpath colvar component")] = "n/a";
00550
00551 feature_count_[std::string("linearCombination colvar component")] = 0;
00552 feature_paper_map_[std::string("linearCombination colvar component")] = "n/a";
00553
00554 feature_count_[std::string("gspathCV colvar component")] = 0;
00555 feature_paper_map_[std::string("gspathCV colvar component")] = "n/a";
00556
00557 feature_count_[std::string("gzpathCV colvar component")] = 0;
00558 feature_paper_map_[std::string("gzpathCV colvar component")] = "n/a";
00559
00560 feature_count_[std::string("aspathCV colvar component")] = 0;
00561 feature_paper_map_[std::string("aspathCV colvar component")] = "n/a";
00562
00563 feature_count_[std::string("azpathCV colvar component")] = 0;
00564 feature_paper_map_[std::string("azpathCV colvar component")] = "n/a";
00565
00566 feature_count_[std::string("coordNum pairlist")] = 0;
00567 feature_paper_map_[std::string("coordNum pairlist")] = "n/a";
00568
00569 feature_count_[std::string("Custom functions (Lepton)")] = 0;
00570 feature_paper_map_[std::string("Custom functions (Lepton)")] = "n/a";
00571
00572 feature_count_[std::string("Scripted functions (Tcl)")] = 0;
00573 feature_paper_map_[std::string("Scripted functions (Tcl)")] = "n/a";
