-
1
-
-
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 (11) 4665-4677 10.1063/1.473503
-
(1997)
J. Chem. Phys.
, vol.106
, Issue.11
, pp. 4665-4677
-
-
Voter, A.F.1
-
2
-
-
0142090170
-
Accelerated Molecular Dynamics with the Bond-Boost Method
-
Miron, R. A.; Fichthorn, K. A. Accelerated Molecular Dynamics with the Bond-Boost Method J. Chem. Phys. 2003, 119 (12) 6210-6216 10.1063/1.1603722
-
(2003)
J. Chem. Phys.
, vol.119
, Issue.12
, pp. 6210-6216
-
-
Miron, R.A.1
Fichthorn, K.A.2
-
4
-
-
72749105901
-
Forward Flux Sampling for Rare Event Simulations
-
Allen, R. J.; Valeriani, C.; Rein Ten Wolde, P. Forward Flux Sampling for Rare Event Simulations J. Phys.: Condens. Matter 2009, 21 (46) 463102 10.1088/0953-8984/21/46/463102
-
(2009)
J. Phys.: Condens. Matter
, vol.21
, Issue.46
, pp. 463102
-
-
Allen, R.J.1
Valeriani, C.2
Rein Ten Wolde, P.3
-
5
-
-
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 (1) 291-318 10.1146/annurev.physchem.53.082301.113146
-
(2002)
Annu. Rev. Phys. Chem.
, vol.53
, Issue.1
, pp. 291-318
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.L.4
-
6
-
-
84973369671
-
Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint
-
Valsson, O.; Tiwary, P.; Parrinello, M. Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint Annu. Rev. Phys. Chem. 2016, 67, 159-184 10.1146/annurev-physchem-040215-112229
-
(2016)
Annu. Rev. Phys. Chem.
, vol.67
, pp. 159-184
-
-
Valsson, O.1
Tiwary, P.2
Parrinello, M.3
-
7
-
-
85011333366
-
Variational Flooding Study of a SN2 Reaction
-
Piccini, G.; McCarty, J.; Valsson, O.; Parrinello, M. Variational Flooding Study of a SN2 Reaction J. Phys. Chem. Lett. 2017, 8 (3) 580-583 10.1021/acs.jpclett.6b02852
-
(2017)
J. Phys. Chem. Lett.
, vol.8
, Issue.3
, pp. 580-583
-
-
Piccini, G.1
McCarty, J.2
Valsson, O.3
Parrinello, M.4
-
8
-
-
84889779905
-
From Metadynamics to Dynamics
-
Tiwary, P.; Parrinello, M. From Metadynamics to Dynamics Phys. Rev. Lett. 2013, 111 (23) 230602 10.1103/PhysRevLett.111.230602
-
(2013)
Phys. Rev. Lett.
, vol.111
, Issue.23
, pp. 230602
-
-
Tiwary, P.1
Parrinello, M.2
-
9
-
-
84955517278
-
A New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations
-
Fleming, K. L.; Tiwary, P.; Pfaendtner, J. A New Approach for Investigating Reaction Dynamics and Rates with Ab Initio Calculations J. Phys. Chem. A 2016, 120 (2) 299-305 10.1021/acs.jpca.5b10667
-
(2016)
J. Phys. Chem. A
, vol.120
, Issue.2
, pp. 299-305
-
-
Fleming, K.L.1
Tiwary, P.2
Pfaendtner, J.3
-
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 (5) E386-E391 10.1073/pnas.1424461112
-
(2015)
Proc. Natl. Acad. Sci. U. S. A.
, vol.112
, Issue.5
, pp. E386-E391
-
-
Tiwary, P.1
Limongelli, V.2
Salvalaglio, M.3
Parrinello, M.4
-
11
-
-
85015157618
-
Kinetics and Mechanism of Ionic-Liquid Induced Protein Unfolding: Application to the Model Protein HP35
-
Tung, H.-J.; Pfaendtner, J. Kinetics and Mechanism of Ionic-Liquid Induced Protein Unfolding: Application to the Model Protein HP35 Mol. Syst. Des. Eng. 2016, 1 (4) 382-390 10.1039/C6ME00047A
-
(2016)
Mol. Syst. Des. Eng.
, vol.1
, Issue.4
, pp. 382-390
-
-
Tung, H.-J.1
Pfaendtner, J.2
-
12
-
-
84964318213
-
Kramers Turnover: From Energy Diffusion to Spatial Diffusion Using Metadynamics
-
Tiwary, P.; Berne, B. J. Kramers Turnover: From Energy Diffusion to Spatial Diffusion Using Metadynamics J. Chem. Phys. 2016, 144 (13) 134103 10.1063/1.4944577
-
(2016)
J. Chem. Phys.
, vol.144
, Issue.13
, pp. 134103
-
-
Tiwary, P.1
Berne, B.J.2
-
13
-
-
84942937974
-
Role of Water and Steric Constraints in the Kinetics of Cavity-Ligand Unbinding
-
Tiwary, P.; Mondal, J.; Morrone, J. A.; Berne, B. J. Role of Water and Steric Constraints in the Kinetics of Cavity-Ligand Unbinding Proc. Natl. Acad. Sci. U. S. A. 2015, 112 (39) 12015-12019 10.1073/pnas.1516652112
-
(2015)
Proc. Natl. Acad. Sci. U. S. A.
, vol.112
, Issue.39
, pp. 12015-12019
-
-
Tiwary, P.1
Mondal, J.2
Morrone, J.A.3
Berne, B.J.4
-
14
-
-
84977566633
-
Using Molecular Simulation to Study Biocatalysis in Ionic Liquids
-
Voth, G. A. Academic Press: Cambridge, MA
-
Sprenger, K. G.; Pfaendtner, J. Using Molecular Simulation to Study Biocatalysis in Ionic Liquids. In Methods in Enzymology; Voth, G. A., Ed.; Academic Press: Cambridge, MA, 2016; Vol. 577, pp 419-441.
-
(2016)
Methods in Enzymology
, vol.577
, pp. 419-441
-
-
Sprenger, K.G.1
Pfaendtner, J.2
-
15
-
-
85009067497
-
Determining Energy Barriers and Selectivities of a Multi-Pathway System with Infrequent Metadynamics
-
Fu, C. D.; Oliveira, L. F. L.; Pfaendtner, J. Determining Energy Barriers and Selectivities of a Multi-Pathway System with Infrequent Metadynamics J. Chem. Phys. 2017, 146 (1) 014108 10.1063/1.4971800
-
(2017)
J. Chem. Phys.
, vol.146
, Issue.1
, pp. 014108
-
-
Fu, C.D.1
Oliveira, L.F.L.2
Pfaendtner, J.3
-
16
-
-
84927740376
-
Bias-Exchange Metadynamics Simulations: An Efficient Strategy for the Analysis of Conduction and Selectivity in Ion Channels
-
Domene, C.; Barbini, P.; Furini, S. Bias-Exchange Metadynamics Simulations: An Efficient Strategy for the Analysis of Conduction and Selectivity in Ion Channels J. Chem. Theory Comput. 2015, 11 (4) 1896-1906 10.1021/ct501053x
-
(2015)
J. Chem. Theory Comput.
, vol.11
, Issue.4
, pp. 1896-1906
-
-
Domene, C.1
Barbini, P.2
Furini, S.3
-
17
-
-
84907377430
-
Variational Approach to Enhanced Sampling and Free Energy Calculations
-
Valsson, O.; Parrinello, M. Variational Approach to Enhanced Sampling and Free Energy Calculations Phys. Rev. Lett. 2014, 113 (9) 1-5 10.1103/PhysRevLett.113.090601
-
(2014)
Phys. Rev. Lett.
, vol.113
, Issue.9
, pp. 1-5
-
-
Valsson, O.1
Parrinello, M.2
-
18
-
-
84956895818
-
Enhanced, Targeted Sampling of High-Dimensional Free-Energy Landscapes Using Variationally Enhanced Sampling, with an Application to Chignolin
-
Shaffer, P.; Valsson, O.; Parrinello, M. Enhanced, Targeted Sampling of High-Dimensional Free-Energy Landscapes Using Variationally Enhanced Sampling, with an Application to Chignolin Proc. Natl. Acad. Sci. U. S. A. 2016, 113 (5) 1150-1155 10.1073/pnas.1519712113
-
(2016)
Proc. Natl. Acad. Sci. U. S. A.
, vol.113
, Issue.5
, pp. 1150-1155
-
-
Shaffer, P.1
Valsson, O.2
Parrinello, M.3
-
19
-
-
84946945227
-
Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics
-
Pfaendtner, J.; Bonomi, M. Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics J. Chem. Theory Comput. 2015, 11 (11) 5062-5067 10.1021/acs.jctc.5b00846
-
(2015)
J. Chem. Theory Comput.
, vol.11
, Issue.11
, pp. 5062-5067
-
-
Pfaendtner, J.1
Bonomi, M.2
-
20
-
-
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 (8) 85504 10.1103/PhysRevLett.107.085504
-
(2011)
Phys. Rev. Lett.
, vol.107
, Issue.8
, pp. 85504
-
-
Pietrucci, F.1
Andreoni, W.2
-
21
-
-
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 (10) 4545-4554 10.1021/acs.jctc.5b00597
-
(2015)
J. Chem. Theory Comput.
, vol.11
, Issue.10
, pp. 4545-4554
-
-
Bal, K.M.1
Neyts, E.C.2
-
22
-
-
84875322422
-
Accelerated Molecular Dynamics through Stochastic Iterations and Collective Variable Based Basin Identification
-
Tiwary, P.; Van De Walle, A. Accelerated Molecular Dynamics through Stochastic Iterations and Collective Variable Based Basin Identification Phys. Rev. B: Condens. Matter Mater. Phys. 2013, 87 (9) 1-6 10.1103/PhysRevB.87.094304
-
(2013)
Phys. Rev. B: Condens. Matter Mater. Phys.
, vol.87
, Issue.9
, pp. 1-6
-
-
Tiwary, P.1
Van De Walle, A.2
-
23
-
-
84901373253
-
A CPMD + Metadynamics Study of High Temperature Methanol Oxidation Reactions Using Generic Collective Variables
-
Zheng, S.; Pfaendtner, J. A CPMD + 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
-
24
-
-
84979256253
-
Direct Observation of Realistic-Temperature Fuel Combustion Mechanisms in Atomistic Simulations
-
Bal, K. M.; Neyts, E. C. Direct Observation of Realistic-Temperature Fuel Combustion Mechanisms in Atomistic Simulations Chem. Sci. 2016, 7, 5280-5286 10.1039/C6SC00498A
-
(2016)
Chem. Sci.
, vol.7
, pp. 5280-5286
-
-
Bal, K.M.1
Neyts, E.C.2
-
25
-
-
65549120583
-
Accelerated Molecular Dynamics Simulation of Thin-Film Growth with the Bond-Boost Method
-
Fichthorn, K. A.; Miron, R. A.; Wang, Y.; Tiwary, Y. Accelerated Molecular Dynamics Simulation of Thin-Film Growth with the Bond-Boost Method J. Phys.: Condens. Matter 2009, 21 (8) 084212 10.1088/0953-8984/21/8/084212
-
(2009)
J. Phys.: Condens. Matter
, vol.21
, Issue.8
, pp. 084212
-
-
Fichthorn, K.A.1
Miron, R.A.2
Wang, Y.3
Tiwary, Y.4
-
26
-
-
69349084577
-
Chapter 4 Accelerated Molecular Dynamics Methods: Introduction and Recent Developments
-
Perez, D.; Uberuaga, B. P.; Shim, Y.; Amar, J. G.; Voter, A. F. Chapter 4 Accelerated Molecular Dynamics Methods: Introduction and Recent Developments Annu. Rep. Comput. Chem. 2009, 5, 79-98 10.1016/S1574-1400(09)00504-0
-
(2009)
Annu. Rep. Comput. Chem.
, vol.5
, pp. 79-98
-
-
Perez, D.1
Uberuaga, B.P.2
Shim, Y.3
Amar, J.G.4
Voter, A.F.5
-
27
-
-
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 (4) 1420-1425 10.1021/ct500040r
-
(2014)
J. Chem. Theory Comput.
, vol.10
, Issue.4
, pp. 1420-1425
-
-
Salvalaglio, M.1
Tiwary, P.2
Parrinello, M.3
-
28
-
-
84941871856
-
The Kolmogorov-Smirnov Test for Goodness of Fit
-
Massey, F. J. The Kolmogorov-Smirnov Test for Goodness of Fit J. Am. Stat. Assoc. 1951, 46 (253) 68-78 10.1080/01621459.1951.10500769
-
(1951)
J. Am. Stat. Assoc.
, vol.46
, Issue.253
, pp. 68-78
-
-
Massey, F.J.1
-
29
-
-
35448937584
-
Optimization of Parameters for Semiempirical Methods V: Modification of NDDO Approximations and Application to 70 Elements
-
Stewart, J. 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.J.P.1
-
30
-
-
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 (1-3) 1-41 10.1016/0010-4655(95)00041-D
-
(1995)
Comput. Phys. Commun.
, vol.91
, Issue.13
, 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
-
31
-
-
84888642158
-
PLUMED 2: New Feathers for an Old Bird
-
Tribello, G. A.; Bonomi, M.; Branduardi, D.; Camilloni, C.; Bussi, G. PLUMED 2: New Feathers for an Old Bird Comput. Phys. Commun. 2014, 185 (2) 604-613 10.1016/j.cpc.2013.09.018
-
(2014)
Comput. Phys. Commun.
, vol.185
, Issue.2
, pp. 604-613
-
-
Tribello, G.A.1
Bonomi, M.2
Branduardi, D.3
Camilloni, C.4
Bussi, G.5
-
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 (12) 126601 10.1088/0034-4885/71/12/126601
-
(2008)
Rep. Prog. Phys.
, vol.71
, Issue.12
, pp. 126601
-
-
Laio, A.1
Gervasio, F.L.2
|