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Volumn 7, Issue 4, 2011, Pages 890-897

On the use of accelerated molecular dynamics to enhance configurational sampling in Ab initio simulations

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EID: 79954471368     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct100605v     Document Type: Article
Times cited : (133)

References (34)
  • 1
    • 3142716857 scopus 로고    scopus 로고
    • Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
    • Hamelberg, D.; Mongan, J.; McCammon, J. A. Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules J. Chem. Phys. 2004, 120 (24) 11919
    • (2004) J. Chem. Phys. , vol.120 , Issue.24 , pp. 11919
    • Hamelberg, D.1    Mongan, J.2    McCammon, J.A.3
  • 2
    • 77949709452 scopus 로고    scopus 로고
    • Dissociation of NaCl in water from ab initio molecular dynamics simulations
    • Timko, J.; Bucher, D.; Kuyucak, S. Dissociation of NaCl in water from ab initio molecular dynamics simulations J. Chem. Phys. 2010, 132 (11) 114510
    • (2010) J. Chem. Phys. , vol.132 , Issue.11 , pp. 114510
    • Timko, J.1    Bucher, D.2    Kuyucak, S.3
  • 6
    • 0037156101 scopus 로고    scopus 로고
    • A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations
    • Laio, A.; VandeVondele, J.; Rothlisberger, U. A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations J. Chem. Phys. 2002, 116 (16) 6941
    • (2002) J. Chem. Phys. , vol.116 , Issue.16 , pp. 6941
    • Laio, A.1    Vandevondele, J.2    Rothlisberger, U.3
  • 7
    • 0000729781 scopus 로고    scopus 로고
    • Transition path sampling and the calculation of rate constants
    • Dellago, C.; Bolhuis, P. G.; Csajka, F. S.; Chandler, D. Transition path sampling and the calculation of rate constants J. Chem. Phys. 1998, 108 (5) 1964
    • (1998) J. Chem. Phys. , vol.108 , Issue.5 , pp. 1964
    • Dellago, C.1    Bolhuis, P.G.2    Csajka, F.S.3    Chandler, D.4
  • 8
    • 0027794972 scopus 로고
    • Targeted Molecular-Dynamics Simulation of Conformational Change Application to the T-R Transition in Insulin
    • Schlitter, J.; Engels, M.; Kruger, P.; Jacoby, E.; Wollmer, A. Targeted Molecular-Dynamics Simulation of Conformational Change Application to the T-R Transition in Insulin Mol. Simul. 1993, 10 (2-6) 291
    • (1993) Mol. Simul. , vol.10 , Issue.2-6 , pp. 291
    • Schlitter, J.1    Engels, M.2    Kruger, P.3    Jacoby, E.4    Wollmer, A.5
  • 9
    • 0347929642 scopus 로고
    • Constrained Molecular-Dynamics and the Mean Potential for an Ion-Pair in a Polar-Solvent
    • Ciccotti, G.; Ferrario, M.; Hynes, J. T.; Kapral, R. Constrained Molecular-Dynamics and the Mean Potential for an Ion-Pair in a Polar-Solvent Chem. Phys. 1989, 129 (2) 241
    • (1989) Chem. Phys. , vol.129 , Issue.2 , pp. 241
    • Ciccotti, G.1    Ferrario, M.2    Hynes, J.T.3    Kapral, R.4
  • 11
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 1999, 314 (1-2) 141
    • (1999) Chem. Phys. Lett. , vol.314 , Issue.1-2 , pp. 141
    • Sugita, Y.1    Okamoto, Y.2
  • 13
    • 26444548978 scopus 로고    scopus 로고
    • Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease
    • Hamelberg, D.; McCammon, J. A. Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease J. Am. Chem. Soc. 2005, 127 (40) 13778
    • (2005) J. Am. Chem. Soc. , vol.127 , Issue.40 , pp. 13778
    • Hamelberg, D.1    McCammon, J.A.2
  • 16
    • 63549096871 scopus 로고    scopus 로고
    • Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics
    • Grant, B. J.; Gorfe, A. A.; McCammon, J. A. Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics PLoS Comput. Biol. 2009, 5 (3) e1000325
    • (2009) PLoS Comput. Biol. , vol.5 , Issue.3 , pp. 1000325
    • Grant, B.J.1    Gorfe, A.A.2    McCammon, J.A.3
  • 17
    • 79954455171 scopus 로고    scopus 로고
    • Accelerating Chemical Reactions: Exploring Reactive Free Energy Surfaces Using Accelerated Ab Initio Molecular Dynamics
    • in press.
    • Pierce, L. C. T.; Markwick, R. L.; McCammon, J. A.; Doltsinis, N. L. Accelerating Chemical Reactions: Exploring Reactive Free Energy Surfaces Using Accelerated Ab Initio Molecular Dynamics. J. Chem. Phys. 2010, in press.
    • (2010) J. Chem. Phys.
    • Pierce, L.C.T.1    Markwick, R.L.2    McCammon, J.A.3    Doltsinis, N.L.4
  • 18
    • 38449096891 scopus 로고    scopus 로고
    • Sampling of slow diffusive conformational transitions with accelerated molecular dynamics
    • Hamelberg, D.; de Oliveira, C. A. F.; McCammon, J. A. Sampling of slow diffusive conformational transitions with accelerated molecular dynamics J. Chem. Phys. 2007, 127 (15) 155102
    • (2007) J. Chem. Phys. , vol.127 , Issue.15 , pp. 155102
    • Hamelberg, D.1    De Oliveira, C.A.F.2    McCammon, J.A.3
  • 19
    • 0031144465 scopus 로고    scopus 로고
    • Hyperdynamics: Accelerated molecular dynamics of infrequent events
    • Voter, A. F. Hyperdynamics: Accelerated molecular dynamics of infrequent events Phys. Rev. Lett. 1997, 78 (20) 3908
    • (1997) Phys. Rev. Lett. , vol.78 , Issue.20 , pp. 3908
    • Voter, A.F.1
  • 20
    • 4243606192 scopus 로고
    • 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 (22) 2471
    • (1985) Phys. Rev. Lett. , vol.55 , Issue.22 , pp. 2471
    • Car, R.1    Parrinello, M.2
  • 22
    • 4243553426 scopus 로고
    • 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 (6) 3098
    • (1988) Phys. Rev. A: At., Mol., Opt. Phys. , vol.38 , Issue.6 , pp. 3098
    • Becke, A.D.1
  • 23
    • 0345491105 scopus 로고
    • Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron-Density
    • Lee, C. T.; Yang, W. T.; 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 (2) 785
    • (1988) Phys. Rev. B: Condens. Matter Mater. Phys. , vol.37 , Issue.2 , pp. 785
    • Lee, C.T.1    Yang, W.T.2    Parr, R.G.3
  • 24
    • 0000026966 scopus 로고    scopus 로고
    • Explicit reversible integrators for extended systems dynamics
    • Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein, M. L. Explicit reversible integrators for extended systems dynamics Mol. Phys. 1996, 87 (5) 1117
    • (1996) Mol. Phys. , vol.87 , Issue.5 , pp. 1117
    • Martyna, G.J.1    Tuckerman, M.E.2    Tobias, D.J.3    Klein, M.L.4
  • 26
    • 36449000062 scopus 로고
    • Nose-Hoover Chains - The Canonical Ensemble Via Continuous Dynamics
    • Martyna, G. J.; Klein, M. L.; Tuckerman, M. Nose-Hoover Chains-the Canonical Ensemble Via Continuous Dynamics J. Chem. Phys. 1992, 97 (4) 2635
    • (1992) J. Chem. Phys. , vol.97 , Issue.4 , pp. 2635
    • Martyna, G.J.1    Klein, M.L.2    Tuckerman, M.3
  • 27
    • 0001499074 scopus 로고
    • Spectroscopic Detection of Twist-Boat Conformation of Cyclohexane - Direct Measurement of Free-Energy Difference between Chair and Twist-Boat
    • Squillacote, M.; Sheridan, R. S.; Chapman, O. L.; Anet, F. A. L. Spectroscopic Detection of Twist-Boat Conformation of Cyclohexane-Direct Measurement of Free-Energy Difference between Chair and Twist-Boat J. Am. Chem. Soc. 1975, 97 (11) 3244
    • (1975) J. Am. Chem. Soc. , vol.97 , Issue.11 , pp. 3244
    • Squillacote, M.1    Sheridan, R.S.2    Chapman, O.L.3    Anet, F.A.L.4
  • 28
    • 0013450127 scopus 로고
    • Vibrational-Spectra of Twist-Boat Cyclohexane
    • Offenbach, J. L.; Fredin, L.; Strauss, H. L. Vibrational-Spectra of Twist-Boat Cyclohexane J. Am. Chem. Soc. 1981, 103 (5) 1001
    • (1981) J. Am. Chem. Soc. , vol.103 , Issue.5 , pp. 1001
    • Offenbach, J.L.1    Fredin, L.2    Strauss, H.L.3
  • 29
    • 29944432123 scopus 로고    scopus 로고
    • Conformational study of cis-1,4-di-tert-butylcyclohexane by dynamic NMR spectroscopy and computational methods. Observation of chair and twist-boat conformations
    • Gill, G.; Pawar, D. M.; Noe, E. A. Conformational study of cis-1,4-di-tert-butylcyclohexane by dynamic NMR spectroscopy and computational methods. Observation of chair and twist-boat conformations J. Am. Chem. Soc. 2005, 70 (26) 10726
    • (2005) J. Am. Chem. Soc. , vol.70 , Issue.26 , pp. 10726
    • Gill, G.1    Pawar, D.M.2    Noe, E.A.3
  • 30
    • 0020790363 scopus 로고
    • Nmr-Spectroscopy of Cyclohexane Gas -Phase Conformational Kinetics
    • Ross, B. D.; True, N. S. Nmr-Spectroscopy of Cyclohexane Gas -Phase Conformational Kinetics J. Am. Chem. Soc. 1983, 105 (15) 4871
    • (1983) J. Am. Chem. Soc. , vol.105 , Issue.15 , pp. 4871
    • Ross, B.D.1    True, N.S.2
  • 31
    • 0034317110 scopus 로고    scopus 로고
    • A high-quality x-ray scattering experiment on liquid water at ambient conditions
    • Hura, G.; Sorenson, J. M.; Glaeser, R. M.; Head-Gordon, T. A high-quality x-ray scattering experiment on liquid water at ambient conditions J. Chem. Phys. 2000, 113 (20) 9140
    • (2000) J. Chem. Phys. , vol.113 , Issue.20 , pp. 9140
    • Hura, G.1    Sorenson, J.M.2    Glaeser, R.M.3    Head-Gordon, T.4
  • 32
    • 0942287516 scopus 로고    scopus 로고
    • Temperature-dependent hydrogen-bond geometry in liquid water
    • Modig, K.; Pfrommer, B. G.; Halle, B. Temperature-dependent hydrogen-bond geometry in liquid water Phys. Rev. Lett. 2003, 90 (7) 075502-1
    • (2003) Phys. Rev. Lett. , vol.90 , Issue.7 , pp. 075502-1
    • Modig, K.1    Pfrommer, B.G.2    Halle, B.3
  • 33
    • 0000667359 scopus 로고
    • Untersuchungen Uber Die Kinetik Der Neutralisation
    • Eigen, M.; Demaeyer, L. Untersuchungen Uber Die Kinetik Der Neutralisation Z. Elektrochem. 1955, 59 (10) 986
    • (1955) Z. Elektrochem. , vol.59 , Issue.10 , pp. 986
    • Eigen, M.1    Demaeyer, L.2
  • 34
    • 0000307978 scopus 로고
    • Sodium-Chloride Ion-Pair Interaction in Water - Computer-Simulation
    • Berkowitz, M.; Karim, O. A.; McCammon, J. A.; Rossky, P. J. Sodium-Chloride Ion-Pair Interaction in Water-Computer-Simulation Chem. Phys. Lett. 1984, 105 (6) 577
    • (1984) Chem. Phys. Lett. , vol.105 , Issue.6 , pp. 577
    • Berkowitz, M.1    Karim, O.A.2    McCammon, J.A.3    Rossky, P.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.