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" 00166 "}\n"; 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" 00183 "}\n"; 00184 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" 00216 "}\n"; 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" 00293 " pmid = {26505197},\n" 00294 " url = {https://doi.org/10.1371/journal.pcbi.1004368}\n" 00295 "}\n"; 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")] = ""; 00334 00335 feature_count_[std::string("GROMACS engine")] = 0; 00336 feature_paper_map_[std::string("GROMACS engine")] = "Abraham2015"; 00337 00338 feature_count_[std::string("reweightaMD colvar bias implementation (NAMD)")] = 0; 00339 feature_paper_map_[std::string("reweightaMD colvar bias implementation (NAMD)")] = "Chen2021"; 00340 00341 feature_count_[std::string("neuralNetwork colvar component")] = 0; 00342 feature_paper_map_[std::string("neuralNetwork colvar component")] = "Chen2022"; 00343 00344 feature_count_[std::string("Multiple-walker ABF implementation")] = 0; 00345 feature_paper_map_[std::string("Multiple-walker ABF implementation")] = "Comer2014c"; 00346 00347 feature_count_[std::string("Symmetry-adapted RMSD")] = 0; 00348 feature_paper_map_[std::string("Symmetry-adapted RMSD")] = "Ebrahimi2022"; 00349 00350 feature_count_[std::string("Colvars module")] = 0; 00351 feature_paper_map_[std::string("Colvars module")] = "Fiorin2013"; 00352 00353 feature_count_[std::string("Colvars-NAMD interface")] = 0; 00354 feature_paper_map_[std::string("Colvars-NAMD interface")] = "Fiorin2013"; 00355 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"; 00364 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"; 00367 00368 feature_count_[std::string("distanceZ colvar component")] = 0; 00369 feature_paper_map_[std::string("distanceZ colvar component")] = "Fiorin2013"; 00370 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"; 00373 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"; 00376 00377 feature_count_[std::string("distanceInv colvar component")] = 0; 00378 feature_paper_map_[std::string("distanceInv colvar component")] = "Fiorin2013"; 00379 00380 feature_count_[std::string("angle colvar component")] = 0; 00381 feature_paper_map_[std::string("angle colvar component")] = "Fiorin2013"; 00382 00383 feature_count_[std::string("dihedral colvar component")] = 0; 00384 feature_paper_map_[std::string("dihedral colvar component")] = "Fiorin2013"; 00385 00386 feature_count_[std::string("coordNum colvar component")] = 0; 00387 feature_paper_map_[std::string("coordNum colvar component")] = "Fiorin2013"; 00388 00389 feature_count_[std::string("selfCoordNum colvar component")] = 0; 00390 feature_paper_map_[std::string("selfCoordNum colvar component")] = "Fiorin2013"; 00391 00392 feature_count_[std::string("groupCoord colvar component (derived from distance)")] = 0; 00393 feature_paper_map_[std::string("groupCoord colvar component (derived from distance)")] = "Fiorin2013"; 00394 00395 feature_count_[std::string("hBond colvar component")] = 0; 00396 feature_paper_map_[std::string("hBond colvar component")] = "Fiorin2013"; 00397 00398 feature_count_[std::string("rmsd colvar component")] = 0; 00399 feature_paper_map_[std::string("rmsd colvar component")] = "Fiorin2013"; 00400 00401 feature_count_[std::string("eigenvector colvar component")] = 0; 00402 feature_paper_map_[std::string("eigenvector colvar component")] = "Fiorin2013"; 00403 00404 feature_count_[std::string("gyration colvar component")] = 0; 00405 feature_paper_map_[std::string("gyration colvar component")] = "Fiorin2013"; 00406 00407 feature_count_[std::string("inertia colvar component (derived from gyration)")] = 0; 00408 feature_paper_map_[std::string("inertia colvar component (derived from gyration)")] = "Fiorin2013"; 00409 00410 feature_count_[std::string("inertiaZ colvar component (derived from inertia)")] = 0; 00411 feature_paper_map_[std::string("inertiaZ colvar component (derived from inertia)")] = "Fiorin2013"; 00412 00413 feature_count_[std::string("orientation colvar component")] = 0; 00414 feature_paper_map_[std::string("orientation colvar component")] = "Fiorin2013"; 00415 00416 feature_count_[std::string("Moving frame of reference")] = 0; 00417 feature_paper_map_[std::string("Moving frame of reference")] = "Fiorin2013"; 00418 00419 feature_count_[std::string("Optimal rotation via flexible fitting")] = 0; 00420 feature_paper_map_[std::string("Optimal rotation via flexible fitting")] = "Fiorin2013"; 00421 00422 feature_count_[std::string("orientationAngle colvar component (derived from orientation)")] = 0; 00423 feature_paper_map_[std::string("orientationAngle colvar component (derived from orientation)")] = "Fiorin2013"; 00424 00425 feature_count_[std::string("orientationProj colvar component (derived from orientation)")] = 0; 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";