Efficient Sampling of High-Dimensional …
139
19. Wu D, Fajer MI, Cao L, Cheng X, Yang W (2016) Generalized ensemble sampling of enzyme
reaction free energy pathways. Methods Enzymol 577:57–74
20. Bolhuis PG, Chandler D, Dellago C, Geissler PL (2002) Transition path sampling: throwing
ropes over rough mountain passes, in the dark. Annu Rev Phys Chem 53:291–318
21. Nakamura M, Obata M, Morishita T, Oda T (2014) An ab initio approach to free-energy
reconstruction using logarithmic mean force dynamics. J Chem Phys 140
22. Moritsugu K, Terada T, Kidera A (2010) Scalable free energy calculation of proteins via
multiscale essential sampling. J Chem Phys 133:224105
23. Darve E, Pohorille A (2001) Calculating free energies using average force. J Chem Phys
115:9169–9183
24. Henkelman G, Jónsson H (2000) Improved tangent estimate in the nudged elastic band method
for finding minimum energy paths and saddle points. J Chem Phys 113:9978–9985
25. Fujisaki H, Shiga M, Kidera A (2010) Onsager-Machlup action-based path sampling and
its combination with replica exchange for diffusive and multiple pathways. J Chem Phys
132:134101
26. Glowacki DR, Paci E, Shalashilin DV (2009) Boxed molecular dynamics: a simple and general
technique for accelerating rare event kinetics and mapping free energy in large molecular
systems. J Phys Chem B 113:16603–16611
27. Hansmann UHE, Wille LT (2002) Global optimization by energy landscape paving. Phys Rev
Lett 88:068105
28. Weinan W, Ren W, Vanden-Eijnden E (2002) String method for the study of rare events. Phys
Rev B 66:052301
29. Dellago C, Bolhuis PG, Advanced computer simulation approaches for soft matter sciences,
vol 3, Springer, Berlin, pp 167–233. doi:https://doi.org/10.1007/978-3-540-87706-6_3
30. Fujisaki H, Moritsugu K, Matsunaga Y, Morishita T, Maragliano L (2015) Extended phasespace methods for enhanced sampling in molecular simulations: a review. Front Bioeng
Biotechnol 3:1–10
31. Laio A, Parrinello M, Computer simulations in condensed matter systems: from materials to
chemical biology, vol 1. Springer, Berlin, pp 315–347. doi:https://doi.org/10.1007/3-540-352
73-2_9
32. Rodriguez-Gomez D, Darve E, Pohorille A (2004) Assessing the efficiency of free energy
calculation methods. J Chem Phys 120:3563–3578
33. Kirkpatrick S, Gelatt CD, Vecchi MP (1983) Optimization by simulated annealing. Science
220:671–680
34. Hansmann UHE (1997) Parallel tempering algorithm for conformational studies of biological
molecules. Chem Phys Lett 281:140–150
35. Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding.
Chem Phys Lett. https://doi.org/10.1016/S0009-2614(99)01123-9
36. Affentranger R, Tavernelli I, Di Iorio EE (2006) A novel hamiltonian replica exchange md
protocol to enhance protein conformational space sampling. J Chem Theory Comput 2:217–228
37. Liu P, Kim B, Friesner RA, Berne BJ (2005) Replica exchange with solute tempering: A method
for sampling biological systems in explicit water. Proc Natl Acad Sci 102:13749–13754
38. Rosso L, Mináry P, Zhu Z, Tuckerman ME (2002) On the use of the adiabatic molecular
dynamics technique in the calculation of free energy profiles. J Chem Phys 116:4389–4402
39. Maragliano L, Vanden-Eijnden E (2006) A temperature accelerated method for sampling free
energy and determining reaction pathways in rare events simulations. Chem Phys Lett 426:168–
175
40. Earl DJ, Deem MW (2005) Parallel tempering: theory, applications, and new perspectives.
Phys Chem Chem Phys 7:3910
41. Meloni S, Ciccotti G (2015) Free energies for rare events: temperature accelerated MD and
MC. Eur Phys J Spec Top 224:2389–2407
42. Luitz M, Bomblies R, Ostermeir K, Zacharias M (2015) Exploring biomolecular dynamics and
interactions using advanced sampling methods. J Phys Condens Matter 27:323101
139
19. Wu D, Fajer MI, Cao L, Cheng X, Yang W (2016) Generalized ensemble sampling of enzyme
reaction free energy pathways. Methods Enzymol 577:57–74
20. Bolhuis PG, Chandler D, Dellago C, Geissler PL (2002) Transition path sampling: throwing
ropes over rough mountain passes, in the dark. Annu Rev Phys Chem 53:291–318
21. Nakamura M, Obata M, Morishita T, Oda T (2014) An ab initio approach to free-energy
reconstruction using logarithmic mean force dynamics. J Chem Phys 140
22. Moritsugu K, Terada T, Kidera A (2010) Scalable free energy calculation of proteins via
multiscale essential sampling. J Chem Phys 133:224105
23. Darve E, Pohorille A (2001) Calculating free energies using average force. J Chem Phys
115:9169–9183
24. Henkelman G, Jónsson H (2000) Improved tangent estimate in the nudged elastic band method
for finding minimum energy paths and saddle points. J Chem Phys 113:9978–9985
25. Fujisaki H, Shiga M, Kidera A (2010) Onsager-Machlup action-based path sampling and
its combination with replica exchange for diffusive and multiple pathways. J Chem Phys
132:134101
26. Glowacki DR, Paci E, Shalashilin DV (2009) Boxed molecular dynamics: a simple and general
technique for accelerating rare event kinetics and mapping free energy in large molecular
systems. J Phys Chem B 113:16603–16611
27. Hansmann UHE, Wille LT (2002) Global optimization by energy landscape paving. Phys Rev
Lett 88:068105
28. Weinan W, Ren W, Vanden-Eijnden E (2002) String method for the study of rare events. Phys
Rev B 66:052301
29. Dellago C, Bolhuis PG, Advanced computer simulation approaches for soft matter sciences,
vol 3, Springer, Berlin, pp 167–233. doi:https://doi.org/10.1007/978-3-540-87706-6_3
30. Fujisaki H, Moritsugu K, Matsunaga Y, Morishita T, Maragliano L (2015) Extended phasespace methods for enhanced sampling in molecular simulations: a review. Front Bioeng
Biotechnol 3:1–10
31. Laio A, Parrinello M, Computer simulations in condensed matter systems: from materials to
chemical biology, vol 1. Springer, Berlin, pp 315–347. doi:https://doi.org/10.1007/3-540-352
73-2_9
32. Rodriguez-Gomez D, Darve E, Pohorille A (2004) Assessing the efficiency of free energy
calculation methods. J Chem Phys 120:3563–3578
33. Kirkpatrick S, Gelatt CD, Vecchi MP (1983) Optimization by simulated annealing. Science
220:671–680
34. Hansmann UHE (1997) Parallel tempering algorithm for conformational studies of biological
molecules. Chem Phys Lett 281:140–150
35. Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding.
Chem Phys Lett. https://doi.org/10.1016/S0009-2614(99)01123-9
36. Affentranger R, Tavernelli I, Di Iorio EE (2006) A novel hamiltonian replica exchange md
protocol to enhance protein conformational space sampling. J Chem Theory Comput 2:217–228
37. Liu P, Kim B, Friesner RA, Berne BJ (2005) Replica exchange with solute tempering: A method
for sampling biological systems in explicit water. Proc Natl Acad Sci 102:13749–13754
38. Rosso L, Mináry P, Zhu Z, Tuckerman ME (2002) On the use of the adiabatic molecular
dynamics technique in the calculation of free energy profiles. J Chem Phys 116:4389–4402
39. Maragliano L, Vanden-Eijnden E (2006) A temperature accelerated method for sampling free
energy and determining reaction pathways in rare events simulations. Chem Phys Lett 426:168–
175
40. Earl DJ, Deem MW (2005) Parallel tempering: theory, applications, and new perspectives.
Phys Chem Chem Phys 7:3910
41. Meloni S, Ciccotti G (2015) Free energies for rare events: temperature accelerated MD and
MC. Eur Phys J Spec Top 224:2389–2407
42. Luitz M, Bomblies R, Ostermeir K, Zacharias M (2015) Exploring biomolecular dynamics and
interactions using advanced sampling methods. J Phys Condens Matter 27:323101