-
1
-
-
84892738066
-
Chemical Kinetics and Mechanisms of Complex Systems: A Perspective on Recent Theoretical Advances
-
Klippenstein, S. J.; Pande, V. S.; Truhlar, D. G. Chemical Kinetics and Mechanisms of Complex Systems: A Perspective on Recent Theoretical Advances J. Am. Chem. Soc. 2014, 136, 528-546 10.1021/ja408723a
-
(2014)
J. Am. Chem. Soc.
, vol.136
, pp. 528-546
-
-
Klippenstein, S.J.1
Pande, V.S.2
Truhlar, D.G.3
-
3
-
-
84875760613
-
Metadynamics
-
Barducci, A.; Bonomi, M.; Parrinello, M. Metadynamics WIREs Comput. Mol. Sci. 2011, 1, 826-843 10.1002/wcms.31
-
(2011)
WIREs Comput. Mol. Sci.
, vol.1
, pp. 826-843
-
-
Barducci, A.1
Bonomi, M.2
Parrinello, M.3
-
4
-
-
84902817448
-
Well-Tempered Metadynamics Converges Asymptotically
-
Dama, J. F.; Parrinello, M.; Voth, G. A. Well-Tempered Metadynamics Converges Asymptotically Phys. Rev. Lett. 2014, 112, 240602 10.1103/PhysRevLett.112.240602
-
(2014)
Phys. Rev. Lett.
, vol.112
, pp. 240602
-
-
Dama, J.F.1
Parrinello, M.2
Voth, G.A.3
-
5
-
-
84903938993
-
Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics
-
Iannuzzi, M.; Laio, A.; Parrinello, M. Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics Phys. Rev. Lett. 2003, 90, 238302 10.1103/PhysRevLett.90.238302
-
(2003)
Phys. Rev. Lett.
, vol.90
, pp. 238302
-
-
Iannuzzi, M.1
Laio, A.2
Parrinello, M.3
-
6
-
-
33644968698
-
Metadynamics as a Tool for Exploring Free Energy Landscapes of Chemical Reactions
-
Ensing, B.; De Vivo, M.; Liu, Z.; Moore, P.; Klein, M. L. Metadynamics as a Tool for Exploring Free Energy Landscapes of Chemical Reactions Acc. Chem. Res. 2006, 39, 73-81 10.1021/ar040198i
-
(2006)
Acc. Chem. Res.
, vol.39
, pp. 73-81
-
-
Ensing, B.1
De Vivo, M.2
Liu, Z.3
Moore, P.4
Klein, M.L.5
-
7
-
-
58149299971
-
Metadynamics: A Method to Simulate Rare Events and Reconstruct the Free Energy in Biophysics, Chemistry and Material Science
-
Laio, A.; Gervasio, F. L. Metadynamics: A Method to Simulate Rare Events and Reconstruct the Free Energy in Biophysics, Chemistry and Material Science Rep. Prog. Phys. 2008, 71, 126601 10.1088/0034-4885/71/12/126601
-
(2008)
Rep. Prog. Phys.
, vol.71
, pp. 126601
-
-
Laio, A.1
Gervasio, F.L.2
-
8
-
-
84926210854
-
Enhanced Sampling of Chemical and Biochemical Reactions with Metadynamics
-
Zheng, S.; Pfaendtner, J. Enhanced Sampling of Chemical and Biochemical Reactions with Metadynamics Mol. Simul. 2015, 41, 55-72 10.1080/08927022.2014.923574
-
(2015)
Mol. Simul.
, vol.41
, pp. 55-72
-
-
Zheng, S.1
Pfaendtner, J.2
-
9
-
-
84889779905
-
From Metadynamics to Dynamics
-
Tiwary, P.; Parrinello, M. From Metadynamics to Dynamics Phys. Rev. Lett. 2013, 111, 230602 10.1103/PhysRevLett.111.230602
-
(2013)
Phys. Rev. Lett.
, vol.111
, pp. 230602
-
-
Tiwary, P.1
Parrinello, M.2
-
10
-
-
84922224593
-
Kinetics of Protein-Ligand Unbinding: Predicting Pathways, Rates, and Rate-Limiting Steps
-
Tiwary, P.; Limongelli, V.; Salvalaglio, M.; Parrinello, M. Kinetics of Protein-Ligand Unbinding: Predicting Pathways, Rates, and Rate-Limiting Steps Proc. Natl. Acad. Sci. U. S. A. 2015, 112, E386-E391 10.1073/pnas.1424461112
-
(2015)
Proc. Natl. Acad. Sci. U. S. A.
, vol.112
, pp. E386-E391
-
-
Tiwary, P.1
Limongelli, V.2
Salvalaglio, M.3
Parrinello, M.4
-
11
-
-
84942937974
-
Role of Water and Steric Constraints in the Kinetics of Cavity-Ligand Unbinding
-
Tiwary, P.; Mondal, J.; Morrone, J. A.; Berne, B. Role of Water and Steric Constraints in the Kinetics of Cavity-Ligand Unbinding Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 12015-12019 10.1073/pnas.1516652112
-
(2015)
Proc. Natl. Acad. Sci. U. S. A.
, vol.112
, pp. 12015-12019
-
-
Tiwary, P.1
Mondal, J.2
Morrone, J.A.3
Berne, B.4
-
12
-
-
84898429568
-
Assessing the Reliability of the Dynamics Reconstructed from Metadynamics
-
Salvalaglio, M.; Tiwary, P.; Parrinello, M. Assessing the Reliability of the Dynamics Reconstructed from Metadynamics J. Chem. Theory Comput. 2014, 10, 1420-1425 10.1021/ct500040r
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 1420-1425
-
-
Salvalaglio, M.1
Tiwary, P.2
Parrinello, M.3
-
13
-
-
1442281293
-
A Method for Accelerating the Molecular Dynamics Simulation of Infrequent Events
-
Voter, A. F. A Method for Accelerating the Molecular Dynamics Simulation of Infrequent Events J. Chem. Phys. 1997, 106, 4665-4677 10.1063/1.473503
-
(1997)
J. Chem. Phys.
, vol.106
, pp. 4665-4677
-
-
Voter, A.F.1
-
14
-
-
84944236979
-
Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds
-
Bal, K. M.; Neyts, E. C. Merging Metadynamics into Hyperdynamics: Accelerated Molecular Simulations Reaching Time Scales from Microseconds to Seconds J. Chem. Theory Comput. 2015, 11, 4545-4554 10.1021/acs.jctc.5b00597
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 4545-4554
-
-
Bal, K.M.1
Neyts, E.C.2
-
15
-
-
0036424048
-
Transition Path Sampling: Throwing Ropes over Rough Mountain Passes, in the Dark
-
Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. Transition Path Sampling: Throwing Ropes over Rough Mountain Passes, in the Dark Annu. Rev. Phys. Chem. 2002, 53, 291-318 10.1146/annurev.physchem.53.082301.113146
-
(2002)
Annu. Rev. Phys. Chem.
, vol.53
, pp. 291-318
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.L.4
-
16
-
-
35448937584
-
Optimization of Parameters for Semiempirical Methods V: Modification of Nddo Approximations and Application to 70 Elements
-
Stewart, J. P. Optimization of Parameters for Semiempirical Methods V: Modification of Nddo Approximations and Application to 70 Elements J. Mol. Model. 2007, 13, 1173-1213 10.1007/s00894-007-0233-4
-
(2007)
J. Mol. Model.
, vol.13
, pp. 1173-1213
-
-
Stewart, J.P.1
-
17
-
-
0029633186
-
Amber, a Package of Computer Programs for Applying Molecular Mechanics, Normal Mode Analysis, Molecular Dynamics and Free Energy Calculations to Simulate the Structural and Energetic Properties of Molecules
-
Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E.; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Amber, a Package of Computer Programs for Applying Molecular Mechanics, Normal Mode Analysis, Molecular Dynamics and Free Energy Calculations to Simulate the Structural and Energetic Properties of Molecules Comput. Phys. Commun. 1995, 91, 1-41 10.1016/0010-4655(95)00041-D
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
DeBolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
18
-
-
70450206724
-
-
revision B.01; Gaussian Inc. Wallingford, CT
-
Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; et al., Gaussian 09, revision B.01; Gaussian Inc.: Wallingford, CT, 2009.
-
(2009)
Gaussian 09
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Scalmani, G.7
Barone, V.8
Mennucci, B.9
Petersson, G.A.10
-
19
-
-
4243606192
-
Unified Approach for Molecular Dynamics and Density-Functional Theory
-
Car, R.; Parrinello, M. Unified Approach for Molecular Dynamics and Density-Functional Theory Phys. Rev. Lett. 1985, 55, 2471 10.1103/PhysRevLett.55.2471
-
(1985)
Phys. Rev. Lett.
, vol.55
, pp. 2471
-
-
Car, R.1
Parrinello, M.2
-
20
-
-
0001161603
-
Efficacious Form for Model Pseudopotentials
-
Kleinman, L.; Bylander, D. Efficacious Form for Model Pseudopotentials Phys. Rev. Lett. 1982, 48, 1425 10.1103/PhysRevLett.48.1425
-
(1982)
Phys. Rev. Lett.
, vol.48
, pp. 1425
-
-
Kleinman, L.1
Bylander, D.2
-
21
-
-
4243553426
-
Density-Functional Exchange-Energy Approximation with Correct Asymptotic-Behavior
-
Becke, A. D. Density-Functional Exchange-Energy Approximation with Correct Asymptotic-Behavior Phys. Rev. A: At., Mol., Opt. Phys. 1988, 38, 3098-3100 10.1103/PhysRevA.38.3098
-
(1988)
Phys. Rev. A: At., Mol., Opt. Phys.
, vol.38
, pp. 3098-3100
-
-
Becke, A.D.1
-
22
-
-
0345491105
-
Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density
-
Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density Phys. Rev. B: Condens. Matter Mater. Phys. 1988, 37, 785-789 10.1103/PhysRevB.37.785
-
(1988)
Phys. Rev. B: Condens. Matter Mater. Phys.
, vol.37
, pp. 785-789
-
-
Lee, C.1
Yang, W.2
Parr, R.G.3
-
23
-
-
34547809547
-
A Unified Formulation of the Constant Temperature Molecular-Dynamics Methods
-
Nose, S. A Unified Formulation of the Constant Temperature Molecular-Dynamics Methods J. Chem. Phys. 1984, 81, 511-519 10.1063/1.447334
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 511-519
-
-
Nose, S.1
-
24
-
-
0001538909
-
Canonical Dynamics - Equilibrium Phase-Space Distributions
-
Hoover, W. G. Canonical Dynamics-Equilibrium Phase-Space Distributions Phys. Rev. A: At., Mol., Opt. Phys. 1985, 31, 1695-1697 10.1103/PhysRevA.31.1695
-
(1985)
Phys. Rev. A: At., Mol., Opt. Phys.
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
25
-
-
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. A. et al. Plumed: A Portable Plugin for Free-Energy Calculations with Molecular Dynamics Comput. Phys. Commun. 2009, 180, 1961-1972 10.1016/j.cpc.2009.05.011
-
(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.A.10
-
26
-
-
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, 020603 10.1103/PhysRevLett.100.020603
-
(2008)
Phys. Rev. Lett.
, vol.100
, pp. 020603
-
-
Barducci, A.1
Bussi, G.2
Parrinello, M.3
-
28
-
-
4244179012
-
Frequency Factors and Isotope Effects in Solid State Rate Processes
-
Vineyard, G. H. Frequency Factors and Isotope Effects in Solid State Rate Processes J. Phys. Chem. Solids 1957, 3, 121-127 10.1016/0022-3697(57)90059-8
-
(1957)
J. Phys. Chem. Solids
, vol.3
, pp. 121-127
-
-
Vineyard, G.H.1
-
29
-
-
84907327659
-
A Time-Independent Free Energy Estimator for Metadynamics
-
Tiwary, P.; Parrinello, M. A Time-Independent Free Energy Estimator for Metadynamics J. Phys. Chem. B 2015, 119, 736-742 10.1021/jp504920s
-
(2015)
J. Phys. Chem. B
, vol.119
, pp. 736-742
-
-
Tiwary, P.1
Parrinello, M.2
-
30
-
-
0030955631
-
A Detailed Kinetic Modeling Study of Aromatics Formation in Laminar Premixed Acetylene and Ethylene Flames
-
Wang, H.; Frenklach, M. A Detailed Kinetic Modeling Study of Aromatics Formation in Laminar Premixed Acetylene and Ethylene Flames Combust. Flame 1997, 110, 173-221 10.1016/S0010-2180(97)00068-0
-
(1997)
Combust. Flame
, vol.110
, pp. 173-221
-
-
Wang, H.1
Frenklach, M.2
-
31
-
-
84901373253
-
Car-Parrinello Molecular Dynamics+ Metadynamics Study of High-Temperature Methanol Oxidation Reactions Using Generic Collective Variables
-
Zheng, S.; Pfaendtner, J. Car-Parrinello Molecular Dynamics+ Metadynamics Study of High-Temperature Methanol Oxidation Reactions Using Generic Collective Variables J. Phys. Chem. C 2014, 118, 10764-10770 10.1021/jp500398k
-
(2014)
J. Phys. Chem. C
, vol.118
, pp. 10764-10770
-
-
Zheng, S.1
Pfaendtner, J.2
-
32
-
-
58149299971
-
Metadynamics: A Method to Simulate Rare Events and Reconstruct the Free Energy in Biophysics, Chemistry and Material Science
-
Laio, A.; Gervasio, F. L. Metadynamics: A Method to Simulate Rare Events and Reconstruct the Free Energy in Biophysics, Chemistry and Material Science Rep. Prog. Phys. 2008, 71, 126601 10.1088/0034-4885/71/12/126601
-
(2008)
Rep. Prog. Phys.
, vol.71
, pp. 126601
-
-
Laio, A.1
Gervasio, F.L.2
-
33
-
-
0000160164
-
Separable Dual-Space Gaussian Pseudopotentials
-
Goedecker, S.; Teter, M.; Hutter, J. Separable Dual-Space Gaussian Pseudopotentials Phys. Rev. B: Condens. Matter Mater. Phys. 1996, 54, 1703 10.1103/PhysRevB.54.1703
-
(1996)
Phys. Rev. B: Condens. Matter Mater. Phys.
, vol.54
, pp. 1703
-
-
Goedecker, S.1
Teter, M.2
Hutter, J.3
|