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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"
12 " pages = {19--25},\n"
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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"
33 paper_count_[std::string(
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34 paper_url_[std::string(
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35 paper_bibtex_[std::string(
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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"
44 " pages = {3886--3894},\n"
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51 paper_bibtex_[std::string(
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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"
61 " doi = {10.1021/acs.jcim.1c01010},\n"
62 " URL = {https://doi.org/10.1021/acs.jcim.1c01010}\n"
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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"
76 " pages = {5276--5285},\n"
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78 " pmid = {26583211},\n"
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84 paper_bibtex_[std::string(
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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"
92 " pages = {2494-2502},\n"
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102 "@article{Fiorin2013,\n"
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105 " journal = {Mol. Phys.},\n"
108 " number = {22-23},\n"
109 " pages = {3345--3362},\n"
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121 " title = {Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics},\n"
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156 " title = {New Coarse Variables for the Accurate Determination of Standard Binding Free Energies},\n"
157 " journal = {J. Chem. Theory. Comput.},\n"
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173 " title = {Orientational and Folding Thermodynamics via Electric Dipole Moment Restraining},\n"
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241 " pages = {3676-3685},\n"
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243 " pmid = {27959559},\n"
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270 " title = {Scalable molecular dynamics on {CPU} and {GPU} architectures with {NAMD}},\n"
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288 " journal = {Comp. Phys. Comm.},\n"
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359 " urldate = {2020-09-30},\n"
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490 feature_paper_map_[std::string(
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"Fiorin2013";
492 feature_count_[std::string(
"alpha colvar component")] = 0;
493 feature_paper_map_[std::string(
"alpha colvar component")] =
"Fiorin2013";
495 feature_count_[std::string(
"dihedralPC colvar component")] = 0;
496 feature_paper_map_[std::string(
"dihedralPC colvar component")] =
"Fiorin2013";
498 feature_count_[std::string(
"cartesian colvar component")] = 0;
499 feature_paper_map_[std::string(
"cartesian colvar component")] =
"Fiorin2013";
501 feature_count_[std::string(
"Linear and polynomial combination of colvar components")] = 0;
502 feature_paper_map_[std::string(
"Linear and polynomial combination of colvar components")] =
"Fiorin2013";
504 feature_count_[std::string(
"Metadynamics colvar bias implementation")] = 0;
505 feature_paper_map_[std::string(
"Metadynamics colvar bias implementation")] =
"Fiorin2013";
507 feature_count_[std::string(
"Multiple-walker metadynamics colvar bias implementation")] = 0;
508 feature_paper_map_[std::string(
"Multiple-walker metadynamics colvar bias implementation")] =
"Fiorin2013";
510 feature_count_[std::string(
"Harmonic colvar bias implementation")] = 0;
511 feature_paper_map_[std::string(
"Harmonic colvar bias implementation")] =
"Fiorin2013";
513 feature_count_[std::string(
"harmonicWalls colvar bias implementation")] = 0;
514 feature_paper_map_[std::string(
"harmonicWalls colvar bias implementation")] =
"Fiorin2013";
516 feature_count_[std::string(
"Linear colvar bias implementation")] = 0;
517 feature_paper_map_[std::string(
"Linear colvar bias implementation")] =
"Fiorin2013";
519 feature_count_[std::string(
"Histogram colvar bias implementation")] = 0;
520 feature_paper_map_[std::string(
"Histogram colvar bias implementation")] =
"Fiorin2013";
522 feature_count_[std::string(
"mapTotal colvar component")] = 0;
523 feature_paper_map_[std::string(
"mapTotal colvar component")] =
"Fiorin2020";
525 feature_count_[std::string(
"Volumetric map-based collective variables")] = 0;
526 feature_paper_map_[std::string(
"Volumetric map-based collective variables")] =
"Fiorin2020";
528 feature_count_[std::string(
"Multi-Map collective variables")] = 0;
529 feature_paper_map_[std::string(
"Multi-Map collective variables")] =
"Fiorin2020";
531 feature_count_[std::string(
"Umbrella-integration eABF estimator")] = 0;
532 feature_paper_map_[std::string(
"Umbrella-integration eABF estimator")] =
"Fu2016";
534 feature_count_[std::string(
"polarTheta colvar component")] = 0;
535 feature_paper_map_[std::string(
"polarTheta colvar component")] =
"Fu2017";
537 feature_count_[std::string(
"polarPhi colvar component")] = 0;
538 feature_paper_map_[std::string(
"polarPhi colvar component")] =
"Fu2017";
540 feature_count_[std::string(
"eulerPhi colvar component (derived from orientation_angle)")] = 0;
541 feature_paper_map_[std::string(
"eulerPhi colvar component (derived from orientation_angle)")] =
"Fu2017";
543 feature_count_[std::string(
"eulerTheta colvar component (derived from orientation_angle)")] = 0;
544 feature_paper_map_[std::string(
"eulerTheta colvar component (derived from orientation_angle)")] =
"Fu2017";
546 feature_count_[std::string(
"eulerPsi colvar component (derived from orientation_angle)")] = 0;
547 feature_paper_map_[std::string(
"eulerPsi colvar component (derived from orientation_angle)")] =
"Fu2017";
549 feature_count_[std::string(
"dipoleAngle colvar component")] = 0;
550 feature_paper_map_[std::string(
"dipoleAngle colvar component")] =
"Garate2019";
552 feature_count_[std::string(
"dipoleMagnitude colvar component")] = 0;
553 feature_paper_map_[std::string(
"dipoleMagnitude colvar component")] =
"Garate2019";
555 feature_count_[std::string(
"ABF colvar bias implementation")] = 0;
556 feature_paper_map_[std::string(
"ABF colvar bias implementation")] =
"Henin2010";
558 feature_count_[std::string(
"Internal-forces free energy estimator")] = 0;
559 feature_paper_map_[std::string(
"Internal-forces free energy estimator")] =
"Henin2010";
561 feature_count_[std::string(
"Poisson integration of 2D/3D free energy surfaces")] = 0;
562 feature_paper_map_[std::string(
"Poisson integration of 2D/3D free energy surfaces")] =
"Henin2021";
564 feature_count_[std::string(
"VMD engine")] = 0;
565 feature_paper_map_[std::string(
"VMD engine")] =
"Humphrey1996";
567 feature_count_[std::string(
"eABF implementation")] = 0;
568 feature_paper_map_[std::string(
"eABF implementation")] =
"Lesage2017";
570 feature_count_[std::string(
"CZAR eABF estimator")] = 0;
571 feature_paper_map_[std::string(
"CZAR eABF estimator")] =
"Lesage2017";
573 feature_count_[std::string(
"Ensemble-biased metadynamics (ebMetaD)")] = 0;
574 feature_paper_map_[std::string(
"Ensemble-biased metadynamics (ebMetaD)")] =
"Marinelli2015";
576 feature_count_[std::string(
"NAMD engine")] = 0;
577 feature_paper_map_[std::string(
"NAMD engine")] =
"Phillips2020";
579 feature_count_[std::string(
"Scalable center-of-mass computation (NAMD)")] = 0;
580 feature_paper_map_[std::string(
"Scalable center-of-mass computation (NAMD)")] =
"Phillips2020";
582 feature_count_[std::string(
"LAMMPS engine")] = 0;
583 feature_paper_map_[std::string(
"LAMMPS engine")] =
"Thompson2022";
585 feature_count_[std::string(
"distancePairs colvar component")] = 0;
586 feature_paper_map_[std::string(
"distancePairs colvar component")] =
"Shen2015";
588 feature_count_[std::string(
"histogramRestraint colvar bias implementation")] = 0;
589 feature_paper_map_[std::string(
"histogramRestraint colvar bias implementation")] =
"Shen2015";
591 feature_count_[std::string(
"GridForces volumetric map implementation for NAMD")] = 0;
592 feature_paper_map_[std::string(
"GridForces volumetric map implementation for NAMD")] =
"Wells2007";
594 feature_count_[std::string(
"ALB colvar bias implementation")] = 0;
595 feature_paper_map_[std::string(
"ALB colvar bias implementation")] =
"White2014";
597 feature_count_[std::string(
"OPES")] = 0;
598 feature_paper_map_[std::string(
"OPES")] =
"Invernizzi2020";
600 feature_count_[std::string(
"OPES explore or adaptive kernels")] = 0;
601 feature_paper_map_[std::string(
"OPES explore or adaptive kernels")] =
"Invernizzi2022";
603 feature_count_[std::string(
"Colvars-GROMACS interface")] = 0;
604 feature_paper_map_[std::string(
"Colvars-GROMACS interface")] =
"n/a";
606 feature_count_[std::string(
"gspath colvar component")] = 0;
607 feature_paper_map_[std::string(
"gspath colvar component")] =
"n/a";
609 feature_count_[std::string(
"gzpath colvar component")] = 0;
610 feature_paper_map_[std::string(
"gzpath colvar component")] =
"n/a";
612 feature_count_[std::string(
"linearCombination colvar component")] = 0;
613 feature_paper_map_[std::string(
"linearCombination colvar component")] =
"n/a";
615 feature_count_[std::string(
"gspathCV colvar component")] = 0;
616 feature_paper_map_[std::string(
"gspathCV colvar component")] =
"n/a";
618 feature_count_[std::string(
"gzpathCV colvar component")] = 0;
619 feature_paper_map_[std::string(
"gzpathCV colvar component")] =
"n/a";
621 feature_count_[std::string(
"aspathCV colvar component")] = 0;
622 feature_paper_map_[std::string(
"aspathCV colvar component")] =
"n/a";
624 feature_count_[std::string(
"azpathCV colvar component")] = 0;
625 feature_paper_map_[std::string(
"azpathCV colvar component")] =
"n/a";
627 feature_count_[std::string(
"coordNum pairlist")] = 0;
628 feature_paper_map_[std::string(
"coordNum pairlist")] =
"n/a";
630 feature_count_[std::string(
"Custom functions (Lepton)")] = 0;
631 feature_paper_map_[std::string(
"Custom functions (Lepton)")] =
"n/a";
633 feature_count_[std::string(
"Scripted functions (Tcl)")] = 0;
634 feature_paper_map_[std::string(
"Scripted functions (Tcl)")] =
"n/a";
636 feature_count_[std::string(
"ABMD bias")] = 0;
637 feature_paper_map_[std::string(
"ABMD bias")] =
"n/a";