-
1
-
-
36849039429
-
A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
-
Henzler-Wildman K, Lei M, Thai V, Kerns S, Karplus M, Kern D. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 2007, 450:913-916.
-
(2007)
Nature
, vol.450
, pp. 913-916
-
-
Henzler-Wildman, K.1
Lei, M.2
Thai, V.3
Kerns, S.4
Karplus, M.5
Kern, D.6
-
3
-
-
4243661501
-
Constrained reaction coordinate dynamics for the simulation of rare events
-
Carter EA, Ciccotti G, Hynes JT, Kapral R. Constrained reaction coordinate dynamics for the simulation of rare events. Chem Phys Lett 1989, 156:472-477.
-
(1989)
Chem Phys Lett
, vol.156
, pp. 472-477
-
-
Carter, E.A.1
Ciccotti, G.2
Hynes, J.T.3
Kapral, R.4
-
4
-
-
0023106632
-
Free energy calculation by computer simulation
-
Bash PA, Singh UC, Brown FK, Langridge R, Kollman PA. Free energy calculation by computer simulation. Science 1987, 235:574-576.
-
(1987)
Science
, vol.235
, pp. 574-576
-
-
Bash, P.A.1
Singh, U.C.2
Brown, F.K.3
Langridge, R.4
Kollman, P.A.5
-
5
-
-
0001060458
-
Monte-carlo method for obtaining interionic potential of mean force in ionic solution
-
Patey GN, Valleau JP. Monte-carlo method for obtaining interionic potential of mean force in ionic solution. J Chem Phys 1975, 63:2334-2339.
-
(1975)
J Chem Phys
, vol.63
, pp. 2334-2339
-
-
Patey, G.N.1
Valleau, J.P.2
-
6
-
-
0000689085
-
Predicting slow structural transitions in macromolecular systems: conformational flooding
-
Grubmüller H. Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys Rev E 1995, 52:2893-2906.
-
(1995)
Phys Rev E
, vol.52
, pp. 2893-2906
-
-
Grubmüller, H.1
-
7
-
-
33646987405
-
Optimized Monte Carlo data analysis
-
Ferrenberg A, Swendsen R. Optimized Monte Carlo data analysis. Phys Rev Lett 1989, 63:1195-1198.
-
(1989)
Phys Rev Lett
, vol.63
, pp. 1195-1198
-
-
Ferrenberg, A.1
Swendsen, R.2
-
8
-
-
4243754128
-
Nonequilibrium equality for free energy differences
-
Jarzynski C. Nonequilibrium equality for free energy differences. Phys Rev Lett 1997, 78:2690.
-
(1997)
Phys Rev Lett
, vol.78
, pp. 2690
-
-
Jarzynski, C.1
-
9
-
-
0035935802
-
Calculating free energies using average force
-
Darve E, Pohorille A. Calculating free energies using average force. J Chem Phys 2001, 115:9169-9183.
-
(2001)
J Chem Phys
, vol.115
, pp. 9169-9183
-
-
Darve, E.1
Pohorille, A.2
-
10
-
-
0042852135
-
Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations
-
Gullingsrud J, Braun R, Schulten K. Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. J Comput Phys 1999, 151:190-211.
-
(1999)
J Comput Phys
, vol.151
, pp. 190-211
-
-
Gullingsrud, J.1
Braun, R.2
Schulten, K.3
-
11
-
-
0028710015
-
Local elevation: a method for improving the searching properties of molecular dynamics simulation
-
Huber T, Torda A, van Gunsteren W. Local elevation: a method for improving the searching properties of molecular dynamics simulation. J Comput Aided Mol Des 1994, 8:695-708.
-
(1994)
J Comput Aided Mol Des
, vol.8
, pp. 695-708
-
-
Huber, T.1
Torda, A.2
van Gunsteren, W.3
-
12
-
-
0037085922
-
On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles
-
Rosso L, Minary P, Zhu Z, Tuckerman M. On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles. J Comput Phys 2002, 116:4389-4402.
-
(2002)
J Comput Phys
, vol.116
, pp. 4389-4402
-
-
Rosso, L.1
Minary, P.2
Zhu, Z.3
Tuckerman, M.4
-
14
-
-
38349091489
-
Well-tempered metadynamics: a smoothly converging and tunable free-energy method
-
Barducci A, Bussi G, Parrinello M. Well-tempered metadynamics: a smoothly converging and tunable free-energy method. Phys Rev Lett 2008, 100:20603-4.
-
(2008)
Phys Rev Lett
, vol.100
, pp. 20603-20604
-
-
Barducci, A.1
Bussi, G.2
Parrinello, M.3
-
15
-
-
58149299971
-
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
-
Laio A, Gervasio F. Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Rep Prog Phys 2008, 71:126601.
-
(2008)
Rep Prog Phys
, vol.71
, pp. 126601
-
-
Laio, A.1
Gervasio, F.2
-
17
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995, 117:5179-5197.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
18
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem 2005, 26:1781-1802.
-
(2005)
J Comput Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
19
-
-
46249092554
-
GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess B, Kutzner C, van der Spoel D, Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 2008, 4:435-447.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
van der Spoel, D.3
Lindahl, E.4
-
20
-
-
67650099787
-
ACEMD: accelerating Biomolecular Dynamics in the Microsecond Time Scale
-
Harvey MJ, Giupponi G, Fabritiis GD. ACEMD: accelerating Biomolecular Dynamics in the Microsecond Time Scale. J Chem Theory Comput 2009, 5:1632-1639.
-
(2009)
J Chem Theory Comput
, vol.5
, pp. 1632-1639
-
-
Harvey, M.J.1
Giupponi, G.2
Fabritiis, G.D.3
-
21
-
-
69349100797
-
PLUMED: a portable plugin for free-energy calculations with molecular dynamics
-
Bonomi M, Branduardi D, Bussi G, Camilloni C, Provasi D, Raiteri P, Donadio D, Marinelli F, Pietrucci F, Broglia R. PLUMED: a portable plugin for free-energy calculations with molecular dynamics. Comput Phys Commun 2009, 180:1961-1972.
-
(2009)
Comput Phys Commun
, vol.180
, pp. 1961-1972
-
-
Bonomi, M.1
Branduardi, D.2
Bussi, G.3
Camilloni, C.4
Provasi, D.5
Raiteri, P.6
Donadio, D.7
Marinelli, F.8
Pietrucci, F.9
Broglia, R.10
-
22
-
-
33644772083
-
Equilibrium free energies from nonequilibrium metadynamics
-
Bussi G, Laio A, Parrinello M. Equilibrium free energies from nonequilibrium metadynamics. Phys Rev Lett 2006, 96:090601.
-
(2006)
Phys Rev Lett
, vol.96
, pp. 090601
-
-
Bussi, G.1
Laio, A.2
Parrinello, M.3
-
23
-
-
17444412296
-
Assessing the accuracy of metadynamics
-
Laio A, Rodriguez-Fortea A, Gervasio FL, Ceccarelli M, Parrinello M. Assessing the accuracy of metadynamics. J Phys Chem B 2005, 109:6714-6721.
-
(2005)
J Phys Chem B
, vol.109
, pp. 6714-6721
-
-
Laio, A.1
Rodriguez-Fortea, A.2
Gervasio, F.L.3
Ceccarelli, M.4
Parrinello, M.5
-
24
-
-
33746900781
-
Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations
-
Marsili S, Barducci A, Chelli R, Procacci P, Schettino V. Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations. J Phys Chem B 2006, 110:14011-14013.
-
(2006)
J Phys Chem B
, vol.110
, pp. 14011-14013
-
-
Marsili, S.1
Barducci, A.2
Chelli, R.3
Procacci, P.4
Schettino, V.5
-
25
-
-
21244439384
-
The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge
-
Branduardi D, Gervasio FL, Cavalli A, Recantini M, Parrinello M. The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge. J Am Chem Soc 2005, 127:9147-9155.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 9147-9155
-
-
Branduardi, D.1
Gervasio, F.L.2
Cavalli, A.3
Recantini, M.4
Parrinello, M.5
-
26
-
-
67549127330
-
On the calculation of puckering free energy surfaces
-
Sega M, Autieri E, Pederiva F. On the calculation of puckering free energy surfaces. J Chem Phys 2009, 130:225102.
-
(2009)
J Chem Phys
, vol.130
, pp. 225102
-
-
Sega, M.1
Autieri, E.2
Pederiva, F.3
-
27
-
-
73349098763
-
A collective variable for the efficient exploration of protein beta-sheet structures: application to SH3 and GB1
-
Pietrucci F, Laio A. A collective variable for the efficient exploration of protein beta-sheet structures: application to SH3 and GB1. J Chem Theory Comput 2009, 5:2197-2201.
-
(2009)
J Chem Theory Comput
, vol.5
, pp. 2197-2201
-
-
Pietrucci, F.1
Laio, A.2
-
29
-
-
33750040264
-
Free-energy landscape for hairpin folding from combined parallel tempering and metadynamics
-
Bussi G, Gervasio FL, Laio A, Parrinello M. Free-energy landscape for hairpin folding from combined parallel tempering and metadynamics. J Am Chem Soc 2006, 128:13425-13441.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 13425-13441
-
-
Bussi, G.1
Gervasio, F.L.2
Laio, A.3
Parrinello, M.4
-
30
-
-
77951585445
-
Metadynamics as a tool for mapping the con- formational and free-energy space of peptides-the alanine dipeptide case study
-
Vymetal J, Vondrasek J. Metadynamics as a tool for mapping the con- formational and free-energy space of peptides-the alanine dipeptide case study. J Phys Chem B 2010, 114:5632-5642.
-
(2010)
J Phys Chem B
, vol.114
, pp. 5632-5642
-
-
Vymetal, J.1
Vondrasek, J.2
-
31
-
-
84859756922
-
Graph theory meets ab initio molecular dynamics: atomic structures and transformations at the nanoscale
-
Pietrucci F, Andreoni W. Graph theory meets ab initio molecular dynamics: atomic structures and transformations at the nanoscale. Phys Rev Lett 2011, 107:085504.
-
(2011)
Phys Rev Lett
, vol.107
, pp. 085504
-
-
Pietrucci, F.1
Andreoni, W.2
-
32
-
-
54249091171
-
The unfolded ensemble and folding mechanism of the C-terminal GB1 β-hairpin
-
Bonomi M, Branduardi D, Gervasio F, Parrinello M. The unfolded ensemble and folding mechanism of the C-terminal GB1 β-hairpin. J Am Chem Soc 2008, 130:13938-13944.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 13938-13944
-
-
Bonomi, M.1
Branduardi, D.2
Gervasio, F.3
Parrinello, M.4
-
33
-
-
79959770147
-
A chirality-based metrics for free-energy calculations in biomolecular systems
-
Pietropaolo A, Branduardi D, Bonomi M, Parrinello M. A chirality-based metrics for free-energy calculations in biomolecular systems. J Comput Chem 2011, 32:2627-2637.
-
(2011)
J Comput Chem
, vol.32
, pp. 2627-2637
-
-
Pietropaolo, A.1
Branduardi, D.2
Bonomi, M.3
Parrinello, M.4
-
35
-
-
78651327755
-
Comparing the efficiency of biased and unbiased molecular dynamics in reconstructing the free energy landscape of met-enkephalin
-
Sutto L, D'Abramo M, Luigi Gervasio F. Comparing the efficiency of biased and unbiased molecular dynamics in reconstructing the free energy landscape of met-enkephalin. J Chem Theory Comput 2010, 6:3640-3646.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 3640-3646
-
-
Sutto, L.1
D'Abramo, M.2
Luigi Gervasio, F.3
-
36
-
-
34147097967
-
Metadynamics in essential coordinates: free energy simulation of conformational changes
-
Spiwok V, Lipovov́a P, Kralov́a B. Metadynamics in essential coordinates: free energy simulation of conformational changes. J Phys Chem B 2007, 111:3073-3076.
-
(2007)
J Phys Chem B
, vol.111
, pp. 3073-3076
-
-
Spiwok, V.1
Lipovov́a, P.2
Kralov́a, B.3
-
37
-
-
53149099307
-
Continuous metadynamics in essential coordinates as a tool for free energy modeling of conformational changes
-
Spiwok V, Králov́a B, Tvaroska I. Continuous metadynamics in essential coordinates as a tool for free energy modeling of conformational changes. J Mol Model 2008, 14:995-1002.
-
(2008)
J Mol Model
, vol.14
, pp. 995-1002
-
-
Spiwok, V.1
Králov́a, B.2
Tvaroska, I.3
-
38
-
-
83755206813
-
Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap
-
Spiwok V, Králov́a B. Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap. J Chem Phys 2011, 135, 224504.
-
(2011)
J Chem Phys
, vol.135
, pp. 224504
-
-
Spiwok, V.1
Králov́a, B.2
-
39
-
-
0034704229
-
A global geometric framework for nonlinear dimensionality reduction
-
Tenenbaum J, de Silva V, Langford J. A global geometric framework for nonlinear dimensionality reduction. Science 2000, 290:2319-2323.
-
(2000)
Science
, vol.290
, pp. 2319-2323
-
-
Tenenbaum, J.1
de Silva, V.2
Langford, J.3
-
40
-
-
0031578972
-
Parallel tempering algorithm for conformational studies of biological molecules
-
Hansmann UHE. Parallel tempering algorithm for conformational studies of biological molecules. Chem Phys Lett 1997, 281:140-150.
-
(1997)
Chem Phys Lett
, vol.281
, pp. 140-150
-
-
Hansmann, U.H.E.1
-
41
-
-
0037305918
-
Multiplexed-replica exchange molecular dynamics method for protein folding simulation
-
Rhee YM, Pande VS. Multiplexed-replica exchange molecular dynamics method for protein folding simulation. Biophys J 2003, 84:775-786.
-
(2003)
Biophys J
, vol.84
, pp. 775-786
-
-
Rhee, Y.M.1
Pande, V.S.2
-
42
-
-
73949085678
-
Rapid equilibrium sampling initiated from nonequilibrium data
-
Huang X, Bowman GR, Bacallado S, Pande VS. Rapid equilibrium sampling initiated from nonequilibrium data. Proc Natl Acad Sci USA 2009, 106:19765-19769.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 19765-19769
-
-
Huang, X.1
Bowman, G.R.2
Bacallado, S.3
Pande, V.S.4
-
43
-
-
33644772083
-
Equilibrium free energies from nonequilibrium metadynamics
-
Bussi G, Laio A, Parrinello M. Equilibrium free energies from nonequilibrium metadynamics. Phys Rev Lett 2006, 96:090601.
-
(2006)
Phys Rev Lett
, vol.96
, pp. 090601
-
-
Bussi, G.1
Laio, A.2
Parrinello, M.3
-
44
-
-
79959204416
-
Assessing the quality of the OPEP coarse-grained force field
-
Barducci A, Bonomi M, Derreumaux P. Assessing the quality of the OPEP coarse-grained force field. J Chem Theory Comput 2011, 7:1928-1934.
-
(2011)
J Chem Theory Comput
, vol.7
, pp. 1928-1934
-
-
Barducci, A.1
Bonomi, M.2
Derreumaux, P.3
-
45
-
-
77957937199
-
Atomic-level characterization of the structural dynamics of proteins
-
Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W. Atomic-level characterization of the structural dynamics of proteins. Science 2010, 330:341-346.
-
(2010)
Science
, vol.330
, pp. 341-346
-
-
Shaw, D.E.1
Maragakis, P.2
Lindorff-Larsen, K.3
Piana, S.4
Dror, R.O.5
Eastwood, M.P.6
Bank, J.A.7
Jumper, J.M.8
Salmon, J.K.9
Shan, Y.10
Wriggers, W.11
-
46
-
-
84856694630
-
The different flexibility of c-Src and c-Abl kinases regulates the accessibility of a druggable inactive conformation
-
Lovera S, Sutto L, Boubeva R, Scapozza L, Dölker N, Gervasio F. The different flexibility of c-Src and c-Abl kinases regulates the accessibility of a druggable inactive conformation. J Am Chem Soc 2012, 134:2496-2499.
-
(2012)
J Am Chem Soc
, vol.134
, pp. 2496-2499
-
-
Lovera, S.1
Sutto, L.2
Boubeva, R.3
Scapozza, L.4
Dölker, N.5
Gervasio, F.6
-
47
-
-
84855416769
-
Energy landscape of the prion protein helix 1 probed by metadynamics and NMR
-
Camilloni C, Schaal D, Schweimer K, Schwarzinger S, De Simone A. Energy landscape of the prion protein helix 1 probed by metadynamics and NMR. Biophys J 2012, 102:158-167.
-
(2012)
Biophys J
, vol.102
, pp. 158-167
-
-
Camilloni, C.1
Schaal, D.2
Schweimer, K.3
Schwarzinger, S.4
De Simone, A.5
-
48
-
-
79952267622
-
Finite temperature properties of clusters by replica exchange metadynamics: the water nonamer
-
Zhai Y, Laio A, Tosatti E, Gong XG. Finite temperature properties of clusters by replica exchange metadynamics: the water nonamer. J Am Chem Soc 2011, 133:2535-2540.
-
(2011)
J Am Chem Soc
, vol.133
, pp. 2535-2540
-
-
Zhai, Y.1
Laio, A.2
Tosatti, E.3
Gong, X.G.4
-
49
-
-
78650809380
-
Multicanonical molecular dynamics simulations combined with metadynamics for the free energy landscape of a biomolecular system with high energy barriers
-
Yonezawa Y, Shimoyama H, Nakamura H. Multicanonical molecular dynamics simulations combined with metadynamics for the free energy landscape of a biomolecular system with high energy barriers. Chem Phys Lett 2011, 501:598-602.
-
(2011)
Chem Phys Lett
, vol.501
, pp. 598-602
-
-
Yonezawa, Y.1
Shimoyama, H.2
Nakamura, H.3
-
50
-
-
77952404209
-
Enhanced sampling in the well-tempered ensemble
-
Bonomi M, Parrinello M. Enhanced sampling in the well-tempered ensemble. Phys Rev Lett 2010, 104:190601-190604.
-
(2010)
Phys Rev Lett
, vol.104
, pp. 190601-190604
-
-
Bonomi, M.1
Parrinello, M.2
-
51
-
-
34249071886
-
A bias-exchange approach to protein folding
-
Piana S, Laio A. A bias-exchange approach to protein folding. J Phys Chem B 2007, 111:4553-4559.
-
(2007)
J Phys Chem B
, vol.111
, pp. 4553-4559
-
-
Piana, S.1
Laio, A.2
-
52
-
-
83455244845
-
A hybrid all-atom structure-based model for protein folding and large scale conformational transitions
-
Sutto L, Mereu I, Gervasio FL. A hybrid all-atom structure-based model for protein folding and large scale conformational transitions. J Chem Theory Comput 2011, 7:4208-4217.
-
(2011)
J Chem Theory Comput
, vol.7
, pp. 4208-4217
-
-
Sutto, L.1
Mereu, I.2
Gervasio, F.L.3
-
53
-
-
84855765478
-
Conformational selection versus induced fit in kinases: the case of PI3K-γ
-
D'Abramo M, Rabal O, Oyarzabal J, Gervasio FL. Conformational selection versus induced fit in kinases: the case of PI3K-γ. Angew Chem Int Ed 2012, 51:642-646.
-
(2012)
Angew Chem Int Ed
, vol.51
, pp. 642-646
-
-
D'Abramo, M.1
Rabal, O.2
Oyarzabal, J.3
Gervasio, F.L.4
-
54
-
-
69049084558
-
Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations
-
Pietrucci F, Marinelli F, Carloni P, Laio A. Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations. J Am Chem Soc 2009, 131:11811-11818.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 11811-11818
-
-
Pietrucci, F.1
Marinelli, F.2
Carloni, P.3
Laio, A.4
-
55
-
-
79960220436
-
Combined Metadynamics and umbrella sampling method for the calculation of ion permeation free energy profiles
-
Zhang Y, Voth GA. Combined Metadynamics and umbrella sampling method for the calculation of ion permeation free energy profiles. J Chem Theory Comput 2011, 7:2277-2283.
-
(2011)
J Chem Theory Comput
, vol.7
, pp. 2277-2283
-
-
Zhang, Y.1
Voth, G.A.2
-
56
-
-
0001692244
-
Lambda-dynamics: a new approach to free energy calculations
-
Kong X, Brooks CL. Lambda-dynamics: a new approach to free energy calculations. J Chem Phys 1996, 105:2414.
-
(1996)
J Chem Phys
, vol.105
, pp. 2414
-
-
Kong, X.1
Brooks, C.L.2
-
57
-
-
80052344755
-
Lambda-metadynamics approach to compute absolute solvation free energy
-
Wu P, Hu X, Yang W. Lambda-metadynamics approach to compute absolute solvation free energy. J Phys Chem Lett 2011, 2:2099-2103.
-
(2011)
J Phys Chem Lett
, vol.2
, pp. 2099-2103
-
-
Wu, P.1
Hu, X.2
Yang, W.3
-
58
-
-
52949137003
-
Diffusive reaction dynamics on invariant free energy profiles
-
Krivov SV, M K. Diffusive reaction dynamics on invariant free energy profiles. Proc Natl Acad Sci USA 2008, 105:13841-13846.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 13841-13846
-
-
Krivov, S.V.1
M, K.2
-
60
-
-
41349094233
-
Optimizing the ensemble for equilibration in broad-histogram Monte Carlo simulations
-
Trebst A, Huse DA, Troyer M. Optimizing the ensemble for equilibration in broad-histogram Monte Carlo simulations. Phys Rev E 2004, 70:046701.
-
(2004)
Phys Rev E
, vol.70
, pp. 046701
-
-
Trebst, A.1
Huse, D.A.2
Troyer, M.3
-
63
-
-
80051959824
-
Simplifying the representation of complex free-energy landscapes using sketch-map
-
Ceriotti M, Tribello G, Parrinello M. Simplifying the representation of complex free-energy landscapes using sketch-map. Proc Natl Acad Sci USA 2011, 108:13023-13028.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 13023-13028
-
-
Ceriotti, M.1
Tribello, G.2
Parrinello, M.3
-
64
-
-
67650477115
-
Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics
-
Bonomi M, Barducci A, Parrinello M. Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics. J Comput Chem 2009, 30:1615-1621.
-
(2009)
J Comput Chem
, vol.30
, pp. 1615-1621
-
-
Bonomi, M.1
Barducci, A.2
Parrinello, M.3
-
65
-
-
80055015114
-
METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations
-
Biarńes X, Pietrucci F, Marinelli F, Laio A. METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations. Comput Phys Commun 2012, 183:203-211.
-
(2012)
Comput Phys Commun
, vol.183
, pp. 203-211
-
-
Biarńes, X.1
Pietrucci, F.2
Marinelli, F.3
Laio, A.4
-
68
-
-
77951294588
-
Targeting biomolecular flexibility with metadynamics
-
Leone V, Marinelli F, Carloni P, Parrinello M. Targeting biomolecular flexibility with metadynamics. Curr Opin Struct Biol 2010, 20:148-154.
-
(2010)
Curr Opin Struct Biol
, vol.20
, pp. 148-154
-
-
Leone, V.1
Marinelli, F.2
Carloni, P.3
Parrinello, M.4
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