Collective Variables Module - Developer Documentation
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1
2 paper_count_[std::string("Abraham2015")] = 0;
3 paper_url_[std::string("Abraham2015")] = "https://doi.org/10.1016/j.softx.2015.06.001";
4 paper_bibtex_[std::string("Abraham2015")] =
5 "\n"
6 "@article{Abraham2015,\n"
7 " title = {{GROMACS}: High performance molecular simulations through multi-level parallelism from laptops to supercomputers},\n"
8 " 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"
9 " journal = {{SoftwareX}},\n"
10 " volume = {1--2},\n"
11 " year = {2015},\n"
12 " pages = {19--25},\n"
13 " doi = {10.1016/j.softx.2015.06.001},\n"
14 " url = {https://doi.org/10.1016/j.softx.2015.06.001}\n"
15 "}\n";
16
17 paper_count_[std::string("BouRabee2010")] = 0;
18 paper_url_[std::string("BouRabee2010")] = "https://doi.org/10.1137/090758842";
19 paper_bibtex_[std::string("BouRabee2010")] =
20 "\n"
21 "@article{BouRabee2010,\n"
22 " doi = {10.1137/090758842},\n"
23 " url = {https://doi.org/10.1137/090758842},\n"
24 " year = {2010},\n"
25 " volume = {48},\n"
26 " number = {1},\n"
27 " pages = {278--297},\n"
28 " author = {Nawaf Bou-Rabee and Houman Owhadi},\n"
29 " title = {Long-Run Accuracy of Variational Integrators in the Stochastic Context},\n"
30 " journal = {{SIAM} Journal on Numerical Analysis}\n"
31 "}\n";
32
33 paper_count_[std::string("Chen2021")] = 0;
34 paper_url_[std::string("Chen2021")] = "https://doi.org/10.1021/acs.jctc.1c00103";
35 paper_bibtex_[std::string("Chen2021")] =
36 "\n"
37 "@article{Chen2021,\n"
38 " author = {Chen, Haochuan and Fu, Haohao and Chipot, Christophe and Shao, Xueguang and Cai, Wensheng},\n"
39 " title = {Overcoming free-energy barriers with a seamless combination of a biasing force and a collective variable-independent boost potential},\n"
40 " journal = {J. Chem. Theory Comput.},\n"
41 " year = {2021},\n"
42 " volume = {17},\n"
43 " number = {7},\n"
44 " pages = {3886--3894},\n"
45 " doi = {10.1021/acs.jctc.1c00103},\n"
46 " url = {https://doi.org/10.1021/acs.jctc.1c00103}\n"
47 "}\n";
48
49 paper_count_[std::string("Chen2022")] = 0;
50 paper_url_[std::string("Chen2022")] = "https://doi.org/10.1021/acs.jcim.1c01010";
51 paper_bibtex_[std::string("Chen2022")] =
52 "\n"
53 "@article{Chen2022,\n"
54 " author = {Chen, Haochuan and Liu, Han and Feng, Heying and Fu, Haohao and Cai, Wensheng and Shao, Xueguang and Chipot, Christophe},\n"
55 " title = {MLCV: {Bridging} {Machine-Learning-Based} {Dimensionality} {Reduction} and {Free-Energy} {Calculation}},\n"
56 " journal = {J. Chem. Inf. Model.},\n"
57 " volume = {62},\n"
58 " number = {1},\n"
59 " pages = {1-8},\n"
60 " year = {2022},\n"
61 " doi = {10.1021/acs.jcim.1c01010},\n"
62 " URL = {https://doi.org/10.1021/acs.jcim.1c01010}\n"
63 "}\n";
64
65 paper_count_[std::string("Comer2014c")] = 0;
66 paper_url_[std::string("Comer2014c")] = "https://doi.org/10.1021/ct500874p";
67 paper_bibtex_[std::string("Comer2014c")] =
68 "\n"
69 "@article{Comer2014c,\n"
70 " author = {Comer, Jeffrey and Phillips, James C.{} and Schulten, Klaus and Chipot, Christophe},\n"
71 " title = {Multiple-walker strategies for free-energy calculations in {NAMD}: {Shared} adaptive biasing force and walker selection rules},\n"
72 " journal = {J. Chem. Theor. Comput.},\n"
73 " year = {2014},\n"
74 " volume = {10},\n"
75 " number = {12},\n"
76 " pages = {5276--5285},\n"
77 " doi = {10.1021/ct500874p},\n"
78 " pmid = {26583211},\n"
79 " url = {https://doi.org/10.1021/ct500874p}\n"
80 "}\n";
81
82 paper_count_[std::string("Ebrahimi2022")] = 0;
83 paper_url_[std::string("Ebrahimi2022")] = "https://doi.org/10.1021/acs.jctc.1c01235";
84 paper_bibtex_[std::string("Ebrahimi2022")] =
85 "\n"
86 "@article {Ebrahimi2022,\n"
87 " author = {Ebrahimi, Mina and H\\'enin, J\\'er\\^ome},\n"
88 " title = {Symmetry-Adapted Restraints for Binding Free Energy Calculations},\n"
89 " journal = {Journal of Chemical Theory and Computation},\n"
90 " volume = {18},\n"
91 " number = {4},\n"
92 " pages = {2494-2502},\n"
93 " year = {2022},\n"
94 " doi = {10.1021/acs.jctc.1c01235},\n"
95 " url = {https://doi.org/10.1021/acs.jctc.1c01235}\n"
96 "}\n";
97
98 paper_count_[std::string("Fiorin2013")] = 0;
99 paper_url_[std::string("Fiorin2013")] = "https://doi.org/10.1080/00268976.2013.813594";
100 paper_bibtex_[std::string("Fiorin2013")] =
101 "\n"
102 "@article{Fiorin2013,\n"
103 " author = {Fiorin, Giacomo and Klein, Michael L.{} and H\\'enin, J\\'er\\^ome},\n"
104 " title = {Using collective variables to drive molecular dynamics simulations},\n"
105 " journal = {Mol. Phys.},\n"
106 " year = {2013},\n"
107 " volume = {111},\n"
108 " number = {22-23},\n"
109 " pages = {3345--3362},\n"
110 " publisher = {Taylor & Francis},\n"
111 " doi = {10.1080/00268976.2013.813594},\n"
112 " url = {https://doi.org/10.1080/00268976.2013.813594}\n"
113 "}\n";
114
115 paper_count_[std::string("Fiorin2020")] = 0;
116 paper_url_[std::string("Fiorin2020")] = "https://doi.org/10.1002/jcc.26075";
117 paper_bibtex_[std::string("Fiorin2020")] =
118 "\n"
119 "@article{Fiorin2020,\n"
120 " author = {Fiorin, Giacomo and Marinelli, Fabrizio and {Faraldo-G\\'omez}, Jos\\'e D.},\n"
121 " title = {Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics},\n"
122 " journal = {J. Comp. Chem.},\n"
123 " year = {2020},\n"
124 " volume = {41},\n"
125 " number = {5},\n"
126 " pages = {449--459},\n"
127 " doi = {10.1002/jcc.26075},\n"
128 " pmid = {31602694},\n"
129 " url = {https://doi.org/10.1002/jcc.26075}\n"
130 "}\n";
131
132 paper_count_[std::string("Fiorin2024")] = 0;
133 paper_url_[std::string("Fiorin2024")] = "https://doi.org/10.1021/acs.jpcb.4c05604";
134 paper_bibtex_[std::string("Fiorin2024")] =
135 "\n"
136 "@article{Fiorin2024,\n"
137 " 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},\n"
138 " title = {Expanded Functionality and Portability for the Colvars Library},\n"
139 " journal = {J. Phys. Chem. {B}},\n"
140 " volume = {128},\n"
141 " number = {45},\n"
142 " pages = {11108--11123},\n"
143 " year = {2024},\n"
144 " doi = {10.1021/acs.jpcb.4c05604},\n"
145 " pmid = 39501453,\n"
146 " url = { https://doi.org/10.1021/acs.jpcb.4c05604}\n"
147 "}\n";
148
149 paper_count_[std::string("Fu2016")] = 0;
150 paper_url_[std::string("Fu2016")] = "https://doi.org/10.1021/acs.jctc.6b00447";
151 paper_bibtex_[std::string("Fu2016")] =
152 "\n"
153 "@article{Fu2016,\n"
154 " author = {Fu, Haohao and Shao, Xueguang and Chipot, Christophe and Cai, Wensheng},\n"
155 " title = {Extended adaptive biasing force algorithm. {An} on--the--fly implementation for accurate free--energy calculations},\n"
156 " journal = {J. Chem. Theory Comput.},\n"
157 " year = {2016},\n"
158 " volume = {12},\n"
159 " number = {8},\n"
160 " pages = {3506-–3513},\n"
161 " pmid = {27398726},\n"
162 " doi = {10.1021/acs.jctc.6b00447},\n"
163 " pmid = {27398726},\n"
164 " url = {https://doi.org/10.1021/acs.jctc.6b00447}\n"
165 "}\n";
166
167 paper_count_[std::string("Fu2017")] = 0;
168 paper_url_[std::string("Fu2017")] = "https://doi.org/10.1021/acs.jctc.7b00791";
169 paper_bibtex_[std::string("Fu2017")] =
170 "\n"
171 "@article{Fu2017,\n"
172 " author = {Fu, Haohao and Cai, Wensheng and H\\'enin, J\\'er\\^ome and Roux, Beno\\^it and Chipot, Christophe},\n"
173 " title = {New Coarse Variables for the Accurate Determination of Standard Binding Free Energies},\n"
174 " journal = {J. Chem. Theory. Comput.},\n"
175 " year = {2017},\n"
176 " volume = {13},\n"
177 " number = {11},\n"
178 " pages = {5173-5178},\n"
179 " doi = {10.1021/acs.jctc.7b00791},\n"
180 " pmid = {28965398},\n"
181 " url = {https://doi.org/10.1021/acs.jctc.7b00791}\n"
182 "}\n";
183
184 paper_count_[std::string("Garate2019")] = 0;
185 paper_url_[std::string("Garate2019")] = "https://doi.org/10.1021/acs.jpcb.8b09374";
186 paper_bibtex_[std::string("Garate2019")] =
187 "\n"
188 "@article{Garate2019,\n"
189 " author = {Garate, Jos\\'e Antonio and Bernardin, Alejandro and Escalona, Yerko and Yanez, Carlos and English, Niall J.{} and {Perez-Acle}, Tomas},\n"
190 " title = {Orientational and Folding Thermodynamics via Electric Dipole Moment Restraining},\n"
191 " journal = {J. Phys. Chem. {B}},\n"
192 " year = {2019},\n"
193 " volume = {123},\n"
194 " number = {12},\n"
195 " pages = {2599--2608},\n"
196 " doi = {10.1021/acs.jpcb.8b09374},\n"
197 " pmid = {30831028},\n"
198 " url = {https://doi.org/10.1021/acs.jpcb.8b09374}\n"
199 "}\n";
200
201 paper_count_[std::string("Henin2010")] = 0;
202 paper_url_[std::string("Henin2010")] = "https://doi.org/10.1021/ct9004432";
203 paper_bibtex_[std::string("Henin2010")] =
204 "\n"
205 "@article{Henin2010,\n"
206 " author = {H\\'enin, J\\'er\\^ome and Fiorin, Giacomo and Chipot, Christophe and Klein, Michael L.},\n"
207 " title = {Exploring multidimensional free energy landscapes using time-dependent biases on collective variables},\n"
208 " journal = {J. Chem. Theory Comput.},\n"
209 " year = {2010},\n"
210 " volume = {6},\n"
211 " pages = {35-47},\n"
212 " number = {1},\n"
213 " doi = {10.1021/ct9004432},\n"
214 " pmid = {26614317},\n"
215 " url = {https://doi.org/10.1021/ct9004432}\n"
216 "}\n";
217
218 paper_count_[std::string("Henin2021")] = 0;
219 paper_url_[std::string("Henin2021")] = "https://doi.org/10.1021/acs.jctc.1c00593";
220 paper_bibtex_[std::string("Henin2021")] =
221 "\n"
222 "@Article{Henin2021,\n"
223 " author = {H\\'enin, J.},\n"
224 " journal = {J. Chem. Theory Comput.},\n"
225 " title = {Fast and accurate multidimensional free energy integration},\n"
226 " year = {2021},\n"
227 " doi = {10.1021/acs.jctc.1c00593},\n"
228 " url = {https://doi.org/10.1021/acs.jctc.1c00593},\n"
229 "}\n";
230
231 paper_count_[std::string("ChenFDM101")] = 0;
232 paper_url_[std::string("ChenFDM101")] = "https://www.math.uci.edu/~chenlong/226/FDM.pdf";
233 paper_bibtex_[std::string("ChenFDM101")] =
234 "\n"
235 "@misc{ChenFDM101,\n"
236 " author = {Long Chen},\n"
237 " title = {Finite difference methods for Poisson equation},\n"
238 " url = {https://www.math.uci.edu/~chenlong/226/FDM.pdf},\n"
239 "}\n";
240
241 paper_count_[std::string("Humphrey1996")] = 0;
242 paper_url_[std::string("Humphrey1996")] = "https://doi.org/10.1016/0263-7855(96)00018-5";
243 paper_bibtex_[std::string("Humphrey1996")] =
244 "\n"
245 "@article{Humphrey1996,\n"
246 " title = {{VMD}: visual molecular dynamics},\n"
247 " author = {Humphrey, William and Dalke, Andrew and Schulten, Klaus},\n"
248 " journal = {J. Mol. Graph.},\n"
249 " year = {1996},\n"
250 " volume = {14},\n"
251 " number = {1},\n"
252 " pages = {33--38},\n"
253 " doi = {10.1016/0263-7855(96)00018-5},\n"
254 " url = {https://doi.org/10.1016/0263-7855(96)00018-5}\n"
255 "}\n";
256
257 paper_count_[std::string("Lagardere2023")] = 0;
258 paper_url_[std::string("Lagardere2023")] = "https://arxiv.org/abs/2307.08006";
259 paper_bibtex_[std::string("Lagardere2023")] =
260 "\n"
261 "@misc{Lagardere2023,\n"
262 " title={Lambda-ABF: Simplified, Accurate and Cost-effective Alchemical Free Energy Computations},\n"
263 " 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},\n"
264 " year={2023},\n"
265 " eprint={2307.08006},\n"
266 " archivePrefix={arXiv},\n"
267 " primaryClass={physics.chem-ph},\n"
268 " url = {https://arxiv.org/abs/2307.08006}\n"
269 "}\n";
270
271 paper_count_[std::string("Lesage2017")] = 0;
272 paper_url_[std::string("Lesage2017")] = "https://doi.org/10.1021/acs.jpcb.6b10055";
273 paper_bibtex_[std::string("Lesage2017")] =
274 "\n"
275 "@article{Lesage2017,\n"
276 " author = {Lesage, Adrien and Leli\\`evre, Tony and Stoltz, Gabriel and H\\'enin, J\\'er\\^ome},\n"
277 " title = {Smoothed biasing forces yield unbiased free energies with the extended-system adaptive biasing force method},\n"
278 " journal = {J. Phys. Chem. {B}},\n"
279 " year = {2017},\n"
280 " volume = {121},\n"
281 " number = {15},\n"
282 " pages = {3676-3685},\n"
283 " doi = {10.1021/acs.jpcb.6b10055},\n"
284 " pmid = {27959559},\n"
285 " url = {https://doi.org/10.1021/acs.jpcb.6b10055}\n"
286 "}\n";
287
288 paper_count_[std::string("Marinelli2015")] = 0;
289 paper_url_[std::string("Marinelli2015")] = "https://doi.org/10.1016/j.bpj.2015.05.024";
290 paper_bibtex_[std::string("Marinelli2015")] =
291 "\n"
292 "@article{Marinelli2015,\n"
293 " author = {Marinelli, Fabrizio and Faraldo-G\\'omez, Jos\\'e D.},\n"
294 " title = {Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions},\n"
295 " journal = {Biophys. J.},\n"
296 " year = {2015},\n"
297 " volume = {108},\n"
298 " number = {12},\n"
299 " pages = {2779--2782},\n"
300 " doi = {10.1016/j.bpj.2015.05.024},\n"
301 " pmid = {26083917},\n"
302 " url = {https://doi.org/10.1016/j.bpj.2015.05.024}\n"
303 "}\n";
304
305 paper_count_[std::string("Phillips2020")] = 0;
306 paper_url_[std::string("Phillips2020")] = "https://doi.org/10.1063/5.0014475";
307 paper_bibtex_[std::string("Phillips2020")] =
308 "\n"
309 "@article{Phillips2020,\n"
310 " 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"
311 " title = {Scalable molecular dynamics on {CPU} and {GPU} architectures with {NAMD}},\n"
312 " journal = {J. Chem. Phys.},\n"
313 " year = {2020},\n"
314 " volume = {153},\n"
315 " number = {4},\n"
316 " pages = {044130},\n"
317 " doi = {10.1063/5.0014475},\n"
318 " pmid = {32752662},\n"
319 " url = {https://doi.org/10.1063/5.0014475}\n"
320 "}\n";
321
322 paper_count_[std::string("Thompson2022")] = 0;
323 paper_url_[std::string("Thompson2022")] = "https://doi.org/10.1016/j.cpc.2021.108171";
324 paper_bibtex_[std::string("Thompson2022")] =
325 "\n"
326 "@article{Thompson2022,\n"
327 " title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},\n"
328 " 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"
329 " journal = {Comp. Phys. Comm.},\n"
330 " volume = {271},\n"
331 " pages = {108171},\n"
332 " year = {2022},\n"
333 " doi = {10.1016/j.cpc.2021.108171},\n"
334 " url = {https://doi.org/10.1016/j.cpc.2021.108171}\n"
335 "}\n";
336
337 paper_count_[std::string("Shen2015")] = 0;
338 paper_url_[std::string("Shen2015")] = "https://doi.org/10.1371/journal.pcbi.1004368";
339 paper_bibtex_[std::string("Shen2015")] =
340 "\n"
341 "@article{Shen2015,\n"
342 " title = {Structural refinement of proteins by restrained molecular dynamics simulations with non-interacting molecular fragments},\n"
343 " author = {Shen, Rong and Han, Wei and Fiorin, Giacomo and Islam, Shahidul M and Schulten, Klaus and Roux, Beno{\\^\\i}t},\n"
344 " journal = {{PLoS} Comput. Biol.},\n"
345 " volume = {11},\n"
346 " year = {2015},\n"
347 " number = {10},\n"
348 " pages = {e1004368},\n"
349 " doi = {10.1371/journal.pcbi.1004368},\n"
350 " pmid = {26505197},\n"
351 " url = {https://doi.org/10.1371/journal.pcbi.1004368}\n"
352 "}\n";
353
354 paper_count_[std::string("Wells2007")] = 0;
355 paper_url_[std::string("Wells2007")] = "https://doi.org/10.1063/1.2770738";
356 paper_bibtex_[std::string("Wells2007")] =
357 "\n"
358 "@article{Wells2007,\n"
359 " author = {Wells, David B. and Abramkina, Volha and Aksimentiev, Aleksei},\n"
360 " title = {Exploring transmembrane transport through $\\alpha$-hemolysin with grid-steered molecular dynamics},\n"
361 " journal = {J. Chem. Phys.},\n"
362 " year = {2007},\n"
363 " volume = {127},\n"
364 " number = {12},\n"
365 " pages = {125101},\n"
366 " doi = {10.1063/1.2770738},\n"
367 " pmid = {17902937},\n"
368 " url = {https://doi.org/10.1063/1.2770738}\n"
369 "}\n";
370
371 paper_count_[std::string("White2014")] = 0;
372 paper_url_[std::string("White2014")] = "https://doi.org/10.1021/ct500320c";
373 paper_bibtex_[std::string("White2014")] =
374 "\n"
375 "@article{White2014,\n"
376 " author = {White, Andrew D.{} and Voth, Gregory A.{}},\n"
377 " title = {Efficient and minimal method to bias molecular simulations with experimental data},\n"
378 " journal = {J. Chem. Theory Comput.},\n"
379 " year = {2014},\n"
380 " volume = {10},\n"
381 " number = {8},\n"
382 " pages = {3023-–3030},\n"
383 " doi = {10.1021/ct500320c},\n"
384 " pmid = {26588273},\n"
385 " url = {https://doi.org/10.1021/ct500320c}\n"
386 "}\n";
387
388 paper_count_[std::string("Invernizzi2020")] = 0;
389 paper_url_[std::string("Invernizzi2020")] = "https://pubs.acs.org/doi/10.1021/acs.jpclett.0c00497";
390 paper_bibtex_[std::string("Invernizzi2020")] =
391 "\n"
392 "@article{Invernizzi2020,\n"
393 " title = {Rethinking {Metadynamics}: {From} {Bias} {Potentials} to {Probability} {Distributions}},\n"
394 " volume = {11},\n"
395 " issn = {1948-7185, 1948-7185},\n"
396 " shorttitle = {Rethinking {Metadynamics}},\n"
397 " url = {https://pubs.acs.org/doi/10.1021/acs.jpclett.0c00497},\n"
398 " doi = {10.1021/acs.jpclett.0c00497},\n"
399 " number = {7},\n"
400 " urldate = {2020-09-30},\n"
401 " journal = {J. Phys. Chem. Lett.},\n"
402 " author = {Invernizzi, Michele and Parrinello, Michele},\n"
403 " month = apr,\n"
404 " year = {2020},\n"
405 " pages = {2731--2736},\n"
406 "}\n";
407
408 paper_count_[std::string("Invernizzi2022")] = 0;
409 paper_url_[std::string("Invernizzi2022")] = "https://doi.org/10.1021/acs.jctc.2c00152";
410 paper_bibtex_[std::string("Invernizzi2022")] =
411 "\n"
412 "@article{Invernizzi2022,\n"
413 " title = {Exploration vs {Convergence} {Speed} in {Adaptive}-{Bias} {Enhanced} {Sampling}},\n"
414 " volume = {18},\n"
415 " issn = {1549-9618},\n"
416 " url = {https://doi.org/10.1021/acs.jctc.2c00152},\n"
417 " doi = {10.1021/acs.jctc.2c00152},\n"
418 " number = {6},\n"
419 " urldate = {2024-07-02},\n"
420 " journal = {J. Chem. Theory Comput.},\n"
421 " author = {Invernizzi, Michele and Parrinello, Michele},\n"
422 " month = jun,\n"
423 " year = {2022},\n"
424 " pages = {3988--3996},\n"
425 "}\n";
426
427 paper_count_[std::string("n/a")] = 0;
428 paper_url_[std::string("n/a")] = "";
429 paper_bibtex_[std::string("n/a")] = "";
430
431 feature_count_[std::string("GROMACS engine")] = 0;
432 feature_paper_map_[std::string("GROMACS engine")] = "Abraham2015";
433
434 feature_count_[std::string("BAOA integrator")] = 0;
435 feature_paper_map_[std::string("BAOA integrator")] = "BouRabee2010";
436
437 feature_count_[std::string("reweightaMD colvar bias implementation (NAMD)")] = 0;
438 feature_paper_map_[std::string("reweightaMD colvar bias implementation (NAMD)")] = "Chen2021";
439
440 feature_count_[std::string("neuralNetwork colvar component")] = 0;
441 feature_paper_map_[std::string("neuralNetwork colvar component")] = "Chen2022";
442
443 feature_count_[std::string("Multiple-walker ABF implementation")] = 0;
444 feature_paper_map_[std::string("Multiple-walker ABF implementation")] = "Comer2014c";
445
446 feature_count_[std::string("Symmetry-adapted RMSD")] = 0;
447 feature_paper_map_[std::string("Symmetry-adapted RMSD")] = "Ebrahimi2022";
448
449 feature_count_[std::string("Colvars module")] = 0;
450 feature_paper_map_[std::string("Colvars module")] = "Fiorin2013";
451
452 feature_count_[std::string("Colvars-NAMD interface")] = 0;
453 feature_paper_map_[std::string("Colvars-NAMD interface")] = "Fiorin2013";
454
455 feature_count_[std::string("Colvars-LAMMPS interface")] = 0;
456 feature_paper_map_[std::string("Colvars-LAMMPS interface")] = "Fiorin2013";
457
458 feature_count_[std::string("Colvars-VMD interface (command line)")] = 0;
459 feature_paper_map_[std::string("Colvars-VMD interface (command line)")] = "Fiorin2013";
460
461 feature_count_[std::string("distance colvar component")] = 0;
462 feature_paper_map_[std::string("distance colvar component")] = "Fiorin2013";
463
464 feature_count_[std::string("distanceXY colvar component (derived from distanceZ)")] = 0;
465 feature_paper_map_[std::string("distanceXY colvar component (derived from distanceZ)")] = "Fiorin2013";
466
467 feature_count_[std::string("distanceZ colvar component")] = 0;
468 feature_paper_map_[std::string("distanceZ colvar component")] = "Fiorin2013";
469
470 feature_count_[std::string("distanceVec colvar component (derived from distance)")] = 0;
471 feature_paper_map_[std::string("distanceVec colvar component (derived from distance)")] = "Fiorin2013";
472
473 feature_count_[std::string("distanceDir colvar component (derived from distance)")] = 0;
474 feature_paper_map_[std::string("distanceDir colvar component (derived from distance)")] = "Fiorin2013";
475
476 feature_count_[std::string("distanceInv colvar component")] = 0;
477 feature_paper_map_[std::string("distanceInv colvar component")] = "Fiorin2013";
478
479 feature_count_[std::string("angle colvar component")] = 0;
480 feature_paper_map_[std::string("angle colvar component")] = "Fiorin2013";
481
482 feature_count_[std::string("dihedral colvar component")] = 0;
483 feature_paper_map_[std::string("dihedral colvar component")] = "Fiorin2013";
484
485 feature_count_[std::string("coordNum colvar component")] = 0;
486 feature_paper_map_[std::string("coordNum colvar component")] = "Fiorin2013";
487
488 feature_count_[std::string("selfCoordNum colvar component")] = 0;
489 feature_paper_map_[std::string("selfCoordNum colvar component")] = "Fiorin2013";
490
491 feature_count_[std::string("groupCoord colvar component (derived from distance)")] = 0;
492 feature_paper_map_[std::string("groupCoord colvar component (derived from distance)")] = "Fiorin2013";
493
494 feature_count_[std::string("hBond colvar component")] = 0;
495 feature_paper_map_[std::string("hBond colvar component")] = "Fiorin2013";
496
497 feature_count_[std::string("rmsd colvar component")] = 0;
498 feature_paper_map_[std::string("rmsd colvar component")] = "Fiorin2013";
499
500 feature_count_[std::string("eigenvector colvar component")] = 0;
501 feature_paper_map_[std::string("eigenvector colvar component")] = "Fiorin2013";
502
503 feature_count_[std::string("gyration colvar component")] = 0;
504 feature_paper_map_[std::string("gyration colvar component")] = "Fiorin2013";
505
506 feature_count_[std::string("inertia colvar component (derived from gyration)")] = 0;
507 feature_paper_map_[std::string("inertia colvar component (derived from gyration)")] = "Fiorin2013";
508
509 feature_count_[std::string("inertiaZ colvar component (derived from inertia)")] = 0;
510 feature_paper_map_[std::string("inertiaZ colvar component (derived from inertia)")] = "Fiorin2013";
511
512 feature_count_[std::string("orientation colvar component")] = 0;
513 feature_paper_map_[std::string("orientation colvar component")] = "Fiorin2013";
514
515 feature_count_[std::string("Moving frame of reference")] = 0;
516 feature_paper_map_[std::string("Moving frame of reference")] = "Fiorin2013";
517
518 feature_count_[std::string("Optimal rotation via flexible fitting")] = 0;
519 feature_paper_map_[std::string("Optimal rotation via flexible fitting")] = "Fiorin2013";
520
521 feature_count_[std::string("orientationAngle colvar component (derived from orientation)")] = 0;
522 feature_paper_map_[std::string("orientationAngle colvar component (derived from orientation)")] = "Fiorin2013";
523
524 feature_count_[std::string("orientationProj colvar component (derived from orientationAngle)")] = 0;
525 feature_paper_map_[std::string("orientationProj colvar component (derived from orientationAngle)")] = "Fiorin2013";
526
527 feature_count_[std::string("spinAngle colvar component (derived from tilt)")] = 0;
528 feature_paper_map_[std::string("spinAngle colvar component (derived from tilt)")] = "Fiorin2013";
529
530 feature_count_[std::string("tilt colvar component (derived from orientationProj)")] = 0;
531 feature_paper_map_[std::string("tilt colvar component (derived from orientationProj)")] = "Fiorin2013";
532
533 feature_count_[std::string("alpha colvar component")] = 0;
534 feature_paper_map_[std::string("alpha colvar component")] = "Fiorin2013";
535
536 feature_count_[std::string("dihedralPC colvar component")] = 0;
537 feature_paper_map_[std::string("dihedralPC colvar component")] = "Fiorin2013";
538
539 feature_count_[std::string("cartesian colvar component")] = 0;
540 feature_paper_map_[std::string("cartesian colvar component")] = "Fiorin2013";
541
542 feature_count_[std::string("Linear and polynomial combination of colvar components")] = 0;
543 feature_paper_map_[std::string("Linear and polynomial combination of colvar components")] = "Fiorin2013";
544
545 feature_count_[std::string("Metadynamics colvar bias implementation")] = 0;
546 feature_paper_map_[std::string("Metadynamics colvar bias implementation")] = "Fiorin2013";
547
548 feature_count_[std::string("Multiple-walker metadynamics colvar bias implementation")] = 0;
549 feature_paper_map_[std::string("Multiple-walker metadynamics colvar bias implementation")] = "Fiorin2013";
550
551 feature_count_[std::string("Harmonic colvar bias implementation")] = 0;
552 feature_paper_map_[std::string("Harmonic colvar bias implementation")] = "Fiorin2013";
553
554 feature_count_[std::string("harmonicWalls colvar bias implementation")] = 0;
555 feature_paper_map_[std::string("harmonicWalls colvar bias implementation")] = "Fiorin2013";
556
557 feature_count_[std::string("Linear colvar bias implementation")] = 0;
558 feature_paper_map_[std::string("Linear colvar bias implementation")] = "Fiorin2013";
559
560 feature_count_[std::string("Histogram colvar bias implementation")] = 0;
561 feature_paper_map_[std::string("Histogram colvar bias implementation")] = "Fiorin2013";
562
563 feature_count_[std::string("mapTotal colvar component")] = 0;
564 feature_paper_map_[std::string("mapTotal colvar component")] = "Fiorin2020";
565
566 feature_count_[std::string("Volumetric map-based collective variables")] = 0;
567 feature_paper_map_[std::string("Volumetric map-based collective variables")] = "Fiorin2020";
568
569 feature_count_[std::string("Multi-Map collective variables")] = 0;
570 feature_paper_map_[std::string("Multi-Map collective variables")] = "Fiorin2020";
571
572 feature_count_[std::string("Colvars-GROMACS interface")] = 0;
573 feature_paper_map_[std::string("Colvars-GROMACS interface")] = "Fiorin2024";
574
575 feature_count_[std::string("gspath colvar component")] = 0;
576 feature_paper_map_[std::string("gspath colvar component")] = "Fiorin2024";
577
578 feature_count_[std::string("gzpath colvar component")] = 0;
579 feature_paper_map_[std::string("gzpath colvar component")] = "Fiorin2024";
580
581 feature_count_[std::string("linearCombination colvar component")] = 0;
582 feature_paper_map_[std::string("linearCombination colvar component")] = "Fiorin2024";
583
584 feature_count_[std::string("gspathCV colvar component")] = 0;
585 feature_paper_map_[std::string("gspathCV colvar component")] = "Fiorin2024";
586
587 feature_count_[std::string("gzpathCV colvar component")] = 0;
588 feature_paper_map_[std::string("gzpathCV colvar component")] = "Fiorin2024";
589
590 feature_count_[std::string("aspathCV colvar component")] = 0;
591 feature_paper_map_[std::string("aspathCV colvar component")] = "Fiorin2024";
592
593 feature_count_[std::string("azpathCV colvar component")] = 0;
594 feature_paper_map_[std::string("azpathCV colvar component")] = "Fiorin2024";
595
596 feature_count_[std::string("Custom functions (Lepton)")] = 0;
597 feature_paper_map_[std::string("Custom functions (Lepton)")] = "Fiorin2024";
598
599 feature_count_[std::string("Scripted functions (Tcl)")] = 0;
600 feature_paper_map_[std::string("Scripted functions (Tcl)")] = "Fiorin2024";
601
602 feature_count_[std::string("ABMD bias")] = 0;
603 feature_paper_map_[std::string("ABMD bias")] = "Fiorin2024";
604
605 feature_count_[std::string("Updated multiple-walker ABF implementation")] = 0;
606 feature_paper_map_[std::string("Updated multiple-walker ABF implementation")] = "Fiorin2024";
607
608 feature_count_[std::string("Umbrella-integration eABF estimator")] = 0;
609 feature_paper_map_[std::string("Umbrella-integration eABF estimator")] = "Fu2016";
610
611 feature_count_[std::string("polarTheta colvar component")] = 0;
612 feature_paper_map_[std::string("polarTheta colvar component")] = "Fu2017";
613
614 feature_count_[std::string("polarPhi colvar component")] = 0;
615 feature_paper_map_[std::string("polarPhi colvar component")] = "Fu2017";
616
617 feature_count_[std::string("eulerPhi colvar component (derived from orientation_angle)")] = 0;
618 feature_paper_map_[std::string("eulerPhi colvar component (derived from orientation_angle)")] = "Fu2017";
619
620 feature_count_[std::string("eulerTheta colvar component (derived from orientation_angle)")] = 0;
621 feature_paper_map_[std::string("eulerTheta colvar component (derived from orientation_angle)")] = "Fu2017";
622
623 feature_count_[std::string("eulerPsi colvar component (derived from orientation_angle)")] = 0;
624 feature_paper_map_[std::string("eulerPsi colvar component (derived from orientation_angle)")] = "Fu2017";
625
626 feature_count_[std::string("dipoleAngle colvar component")] = 0;
627 feature_paper_map_[std::string("dipoleAngle colvar component")] = "Garate2019";
628
629 feature_count_[std::string("dipoleMagnitude colvar component")] = 0;
630 feature_paper_map_[std::string("dipoleMagnitude colvar component")] = "Garate2019";
631
632 feature_count_[std::string("ABF colvar bias implementation")] = 0;
633 feature_paper_map_[std::string("ABF colvar bias implementation")] = "Henin2010";
634
635 feature_count_[std::string("Internal-forces free energy estimator")] = 0;
636 feature_paper_map_[std::string("Internal-forces free energy estimator")] = "Henin2010";
637
638 feature_count_[std::string("Poisson integration of 2D/3D free energy surfaces")] = 0;
639 feature_paper_map_[std::string("Poisson integration of 2D/3D free energy surfaces")] = "Henin2021";
640
641 feature_count_[std::string("Poisson equation resolution using discrete difference scheme")] = 0;
642 feature_paper_map_[std::string("Poisson equation resolution using discrete difference scheme")] = "ChenFDM101";
643
644 feature_count_[std::string("VMD engine")] = 0;
645 feature_paper_map_[std::string("VMD engine")] = "Humphrey1996";
646
647 feature_count_[std::string("alchLambda colvar component")] = 0;
648 feature_paper_map_[std::string("alchLambda colvar component")] = "Lagardere2023";
649
650 feature_count_[std::string("alchFLambda colvar component")] = 0;
651 feature_paper_map_[std::string("alchFLambda colvar component")] = "Lagardere2023";
652
653 feature_count_[std::string("Tinker-HP interface")] = 0;
654 feature_paper_map_[std::string("Tinker-HP interface")] = "Lagardere2023";
655
656 feature_count_[std::string("eABF implementation")] = 0;
657 feature_paper_map_[std::string("eABF implementation")] = "Lesage2017";
658
659 feature_count_[std::string("CZAR eABF estimator")] = 0;
660 feature_paper_map_[std::string("CZAR eABF estimator")] = "Lesage2017";
661
662 feature_count_[std::string("Ensemble-biased metadynamics (ebMetaD)")] = 0;
663 feature_paper_map_[std::string("Ensemble-biased metadynamics (ebMetaD)")] = "Marinelli2015";
664
665 feature_count_[std::string("NAMD engine")] = 0;
666 feature_paper_map_[std::string("NAMD engine")] = "Phillips2020";
667
668 feature_count_[std::string("Scalable center-of-mass computation (NAMD)")] = 0;
669 feature_paper_map_[std::string("Scalable center-of-mass computation (NAMD)")] = "Phillips2020";
670
671 feature_count_[std::string("LAMMPS engine")] = 0;
672 feature_paper_map_[std::string("LAMMPS engine")] = "Thompson2022";
673
674 feature_count_[std::string("distancePairs colvar component")] = 0;
675 feature_paper_map_[std::string("distancePairs colvar component")] = "Shen2015";
676
677 feature_count_[std::string("histogramRestraint colvar bias implementation")] = 0;
678 feature_paper_map_[std::string("histogramRestraint colvar bias implementation")] = "Shen2015";
679
680 feature_count_[std::string("GridForces volumetric map implementation for NAMD")] = 0;
681 feature_paper_map_[std::string("GridForces volumetric map implementation for NAMD")] = "Wells2007";
682
683 feature_count_[std::string("ALB colvar bias implementation")] = 0;
684 feature_paper_map_[std::string("ALB colvar bias implementation")] = "White2014";
685
686 feature_count_[std::string("OPES")] = 0;
687 feature_paper_map_[std::string("OPES")] = "Invernizzi2020";
688
689 feature_count_[std::string("OPES explore or adaptive kernels")] = 0;
690 feature_paper_map_[std::string("OPES explore or adaptive kernels")] = "Invernizzi2022";
691
692 feature_count_[std::string("coordNum pairlist")] = 0;
693 feature_paper_map_[std::string("coordNum pairlist")] = "n/a";
694
695 feature_count_[std::string("torchANN colvar component")] = 0;
696 feature_paper_map_[std::string("torchANN colvar component")] = "n/a";
Generated on Fri Oct 23 2026 16:44:33 for Collective Variables Module - Developer Documentation by doxygen 1.9.5