version 1.3 | version 1.4 |
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@ARTICLE{Altis2007, | @ARTICLE{Altis2007, |
author = {Altis, Alexandros and Nguyen, Phuong H. and Hegger, Rainer and Stock, | author = {Altis, Alexandros and Nguyen, Phuong H. and Hegger, Rainer and Stock, |
Gerhard}, | Gerhard}, |
| |
number = {9} | number = {9} |
} | } |
| |
| @ARTICLE{Comer2014c, |
| author = {Comer, J. and Phillips, J. and Schulten, K. and Chipot, C.}, |
| title = {Multiple-walker strategies for free-energy calculations in NAMD: |
| Shared adaptive biasing force and walker selection rules}, |
| journal = {J. Chem. Theor. Comput.}, |
| year = {2014}, |
| volume = {10}, |
| pages = {5276-5285}, |
| } |
| |
@ARTICLE{Coutsias2004, | @ARTICLE{Coutsias2004, |
author = {Coutsias, E A and Seok, C and Dill, K A}, | author = {Coutsias, E A and Seok, C and Dill, K A}, |
title = {Using quaternions to calculate {RMSD}}, | title = {Using quaternions to calculate {RMSD}}, |
| |
number = {22-23} | number = {22-23} |
} | } |
| |
| @ARTICLE{Fu2016, |
| author = {Fu, H. and Shao, X. and Chipot, C. and Cai, W.}, |
| title = {Extended adaptive biasing force algorithm. An on--the--fly implementation |
| for accurate free--energy calculations}, |
| journal = {J. Chem. Theory Comput.}, |
| year = {2016}, |
| pmid = {27398726}, |
| url = {http://dx.doi.org/10.1021/acs.jctc.6b00447} |
| } |
| |
@ARTICLE{Glykos2006, | @ARTICLE{Glykos2006, |
author = {Nicholas M Glykos}, | author = {Nicholas M Glykos}, |
title = {Carma: a molecular dynamics analysis program}, | title = {Carma: a molecular dynamics analysis program}, |
| |
number = {23} | number = {23} |
} | } |
| |
| @Article{Kastner2005, |
| Title = {Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: ``Umbrella integration''}, |
| Author = {Kastner, J. and Thiel, W.}, |
| Journal = {J. Chem. Phys.}, |
| Year = {2005}, |
| Number = {14}, |
| Pages = {144104}, |
| Volume = {123}, |
| } |
| |
@ARTICLE{Laio2002, | @ARTICLE{Laio2002, |
author = {Laio, A. and Parrinello, M.}, | author = {Laio, A. and Parrinello, M.}, |
title = {Escaping free-energy minima.}, | title = {Escaping free-energy minima.}, |
| |
number = {20} | number = {20} |
} | } |
| |
| @Article{Lesage2016, |
| author = {Lesage, A. and Leli\`evre, T. and Stoltz, G. and H\'enin, J.}, |
| title = {Smoothed Biasing Forces Yield Unbiased Free Energies With the Extended-System Adaptive Biasing Force Method}, |
| journal = {J. Phys. Chem. B}, |
| note = {(submitted)}, |
| } |
| |
| @ARTICLE{Minoukadeh2010, |
| author = {K. Minoukadeh and C. Chipot and T. Leli\`evre}, |
| title = {Potential of mean force calculations: A multiple-walker adaptive |
| biasing force approach}, |
| journal = {J. Chem. Theor. Comput.}, |
| year = {2010}, |
| volume = {6}, |
| pages = {1008-1017}, |
| } |
| |
@ARTICLE{Mu2005, | @ARTICLE{Mu2005, |
author = {Mu, Yuguang and Nguyen, Phuong H. and Stock, Gerhard}, | author = {Mu, Yuguang and Nguyen, Phuong H. and Stock, Gerhard}, |
title = {Energy landscape of a small peptide revealed by dihedral angle principal | title = {Energy landscape of a small peptide revealed by dihedral angle principal |
| |
} | } |
| |
| |
| @ARTICLE{Shen2015, |
| title={Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments}, |
| author={Shen, Rong and Han, Wei and Fiorin, Giacomo and Islam, Shahidul M and Schulten, Klaus and Roux, Beno{\^\i}t}, |
| journal={{PLoS} Comput. Biol.}, |
| volume={11}, |
| number={10}, |
| pages={e1004368}, |
| year={2015}, |
| publisher={Public Library of Science} |
| } |
| |
| |
@ARTICLE{Pitera2012, | @ARTICLE{Pitera2012, |
author = {Pitera, Jed W. and Chodera, John D.}, | author = {Pitera, Jed W. and Chodera, John D.}, |
| |
year = {2014} | year = {2014} |
| |
} | } |
| |
| @ARTICLE{Zheng2012, |
| author = {L. Zheng and W. Yang}, |
| title = {Practically efficient and robust free energy calculations: Double-integration |
| orthogonal space tempering}, |
| journal = {J. Chem. Theor. Compt.}, |
| year = {2012}, |
| volume = {8}, |
| pages = {810-823}, |
| } |