메뉴 건너뛰기




Volumn 10, Issue 10, 2014, Pages 4198-4207

Computing the free energy along a reaction coordinate using rigid body dynamics

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84907977169     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct500342h     Document Type: Article
Times cited : (14)

References (44)
  • 1
    • 0037171068 scopus 로고    scopus 로고
    • Calculation of free energies from ab initio calculation
    • Ackland, G. J. Calculation of free energies from ab initio calculation J. Phys.: Condens. Matter 2002, 14, 2975-3000
    • (2002) J. Phys.: Condens. Matter , vol.14 , pp. 2975-3000
    • Ackland, G.J.1
  • 2
    • 0037736706 scopus 로고    scopus 로고
    • Free energy calculations. The long and winding gilded road
    • Chipot, C.; Pearlman, D. A. Free energy calculations. The long and winding gilded road Mol. Simul. 2002, 28, 1-12
    • (2002) Mol. Simul. , vol.28 , pp. 1-12
    • Chipot, C.1    Pearlman, D.A.2
  • 4
    • 17544366862 scopus 로고    scopus 로고
    • Free energy methods in molecular simulation
    • Kofke, D. A. Free energy methods in molecular simulation Fluid Phase Equilib. 2005, 228, 41-48
    • (2005) Fluid Phase Equilib. , vol.228 , pp. 41-48
    • Kofke, D.A.1
  • 5
    • 67650485755 scopus 로고    scopus 로고
    • Some Recent Techniques for Free Energy Calculations
    • Vanden-Eijnden, E. Some Recent Techniques for Free Energy Calculations J. Comput. Chem. 2009, 30, 1737-1747
    • (2009) J. Comput. Chem. , vol.30 , pp. 1737-1747
    • Vanden-Eijnden, E.1
  • 6
    • 77952390528 scopus 로고    scopus 로고
    • Basic Ingredients of Free Energy Calculations: A Review
    • Christ, C. D.; Mark, A. E.; van Gunsteren, W. F. Basic Ingredients of Free Energy Calculations: A Review J. Comput. Chem. 2010, 31, 1569-1582
    • (2010) J. Comput. Chem. , vol.31 , pp. 1569-1582
    • Christ, C.D.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 7
    • 33646471468 scopus 로고
    • Statistical Mechanics of Fluid Mixtures
    • Kirkwood, J. G. Statistical Mechanics of Fluid Mixtures J. Chem. Phys. 1935, 3, 300-313
    • (1935) J. Chem. Phys. , vol.3 , pp. 300-313
    • Kirkwood, J.G.1
  • 8
    • 36849122972 scopus 로고
    • High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
    • Zwanzig, R. W. High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases J. Chem. Phys. 1954, 22, 1420-1426
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 10
    • 18644361869 scopus 로고    scopus 로고
    • Free energy profile along a discretized reaction path via the hyperplane constraint force and torque
    • Kudin, K. N.; Car, R. Free energy profile along a discretized reaction path via the hyperplane constraint force and torque J. Chem. Phys. 2005, 122, 114108
    • (2005) J. Chem. Phys. , vol.122 , pp. 114108
    • Kudin, K.N.1    Car, R.2
  • 11
    • 0035584859 scopus 로고    scopus 로고
    • Optimization of hyperplanar transition states
    • Johannesson, G. H.; Jonsson, H. Optimization of hyperplanar transition states J. Chem. Phys. 2001, 115, 9644-9656
    • (2001) J. Chem. Phys. , vol.115 , pp. 9644-9656
    • Johannesson, G.H.1    Jonsson, H.2
  • 12
    • 43949083733 scopus 로고    scopus 로고
    • Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods
    • Hu, H.; Yang, W. T. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods Annu. Rev. Phys. Chem. 2008, 59, 573-601
    • (2008) Annu. Rev. Phys. Chem. , vol.59 , pp. 573-601
    • Hu, H.1    Yang, W.T.2
  • 13
    • 77951688892 scopus 로고    scopus 로고
    • Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events
    • E, W. N.; Vanden-Eijnden, E. Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events Annu. Rev. Phys. Chem. 2010, 61, 391-420
    • (2010) Annu. Rev. Phys. Chem. , vol.61 , pp. 391-420
    • Vanden-Eijnden, E.1
  • 14
    • 79958776843 scopus 로고    scopus 로고
    • Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics/Molecular Mechanics Simulations
    • Rosta, E.; Nowotny, M.; Yang, W.; Hummer, G. Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics/Molecular Mechanics Simulations J. Am. Chem. Soc. 2011, 133, 8934-8941
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 8934-8941
    • Rosta, E.1    Nowotny, M.2    Yang, W.3    Hummer, G.4
  • 15
    • 84884182345 scopus 로고    scopus 로고
    • String Method for Calculation of Minimum Free-Energy Paths in Cartesian Space in Freely Tumbling Systems
    • Branduardi, D.; Faraldo-Gómez, J. D. String Method for Calculation of Minimum Free-Energy Paths in Cartesian Space in Freely Tumbling Systems J. Chem. Theory Comput. 2013, 9, 4140-4154
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 4140-4154
    • Branduardi, D.1    Faraldo-Gómez, J.D.2
  • 16
    • 0001702831 scopus 로고    scopus 로고
    • Free energy from constrained molecular dynamics
    • Sprik, M.; Ciccotti, G. Free energy from constrained molecular dynamics J. Chem. Phys. 1998, 109, 7737-7744
    • (1998) J. Chem. Phys. , vol.109 , pp. 7737-7744
    • Sprik, M.1    Ciccotti, G.2
  • 17
    • 0032529893 scopus 로고    scopus 로고
    • The calculation of free-energy differences by constrained molecular-dynamics simulations
    • den Otter, W. K.; Briels, W. J. The calculation of free-energy differences by constrained molecular-dynamics simulations J. Chem. Phys. 1998, 109, 4139-4146
    • (1998) J. Chem. Phys. , vol.109 , pp. 4139-4146
    • Den Otter, W.K.1    Briels, W.J.2
  • 18
    • 0034691223 scopus 로고    scopus 로고
    • Free energy from molecular dynamics with multiple constraints
    • den Otter, W. K.; Briels, W. J. Free energy from molecular dynamics with multiple constraints Mol. Phys. 2000, 98, 773-781
    • (2000) Mol. Phys. , vol.98 , pp. 773-781
    • Den Otter, W.K.1    Briels, W.J.2
  • 19
    • 0034479196 scopus 로고    scopus 로고
    • Rare events by constrained molecular dynamics
    • Ciccotti, G.; Ferrario, M. Rare events by constrained molecular dynamics J. Mol. Liq. 2000, 89, 1-18
    • (2000) J. Mol. Liq. , vol.89 , pp. 1-18
    • Ciccotti, G.1    Ferrario, M.2
  • 20
    • 1542287930 scopus 로고    scopus 로고
    • Constrained reaction coordinate dynamics for systems with constraints
    • Coluzza, I.; Sprik, M.; Ciccotti, G. Constrained reaction coordinate dynamics for systems with constraints Mol. Phys. 2003, 101, 2885-2894
    • (2003) Mol. Phys. , vol.101 , pp. 2885-2894
    • Coluzza, I.1    Sprik, M.2    Ciccotti, G.3
  • 21
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n -alkanes
    • Ryckaert, J.; Ciccotti, G.; Berendsen, H. J. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n -alkanes J. Comput. Phys. 1977, 23, 327-341
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.1    Ciccotti, G.2    Berendsen, H.J.3
  • 22
    • 0003121620 scopus 로고    scopus 로고
    • Transition-state optimization on free energy surface: Toward solution chemical reaction ergodography
    • Okuyama-Yoshida, N.; Nagaoka, M.; Yamabe, T. Transition-state optimization on free energy surface: Toward solution chemical reaction ergodography Int. J. Quantum Chem. 1998, 70, 95-103
    • (1998) Int. J. Quantum Chem. , vol.70 , pp. 95-103
    • Okuyama-Yoshida, N.1    Nagaoka, M.2    Yamabe, T.3
  • 23
    • 0034269356 scopus 로고    scopus 로고
    • Structure optimization via free energy gradient method: Application to glycine zwitterion in aqueous solution
    • Okuyama-Yoshida, N.; Kataoka, K.; Nagaoka, M.; Yamabe, T. Structure optimization via free energy gradient method: Application to glycine zwitterion in aqueous solution J. Chem. Phys. 2000, 113, 3519-3524
    • (2000) J. Chem. Phys. , vol.113 , pp. 3519-3524
    • Okuyama-Yoshida, N.1    Kataoka, K.2    Nagaoka, M.3    Yamabe, T.4
  • 24
    • 0242289597 scopus 로고    scopus 로고
    • Hydrated structure of ammonia-water molecule pair via the free energy gradient method: Realization of zero gradient and force balance on free energy surfaces
    • Nagae, Y.; Oishi, Y.; Naruse, N.; Nagaoka, M. Hydrated structure of ammonia-water molecule pair via the free energy gradient method: Realization of zero gradient and force balance on free energy surfaces J. Chem. Phys. 2003, 119, 7972-7978
    • (2003) J. Chem. Phys. , vol.119 , pp. 7972-7978
    • Nagae, Y.1    Oishi, Y.2    Naruse, N.3    Nagaoka, M.4
  • 25
    • 33646355962 scopus 로고    scopus 로고
    • Transition-state characterization of the ammonia ionization process in aqueous solution via the free-energy gradient method
    • Nagaoka, M.; Nagae, Y.; Koyano, Y.; Oishi, Y. Transition-state characterization of the ammonia ionization process in aqueous solution via the free-energy gradient method J. Phys. Chem. A 2006, 110, 4555-4563
    • (2006) J. Phys. Chem. A , vol.110 , pp. 4555-4563
    • Nagaoka, M.1    Nagae, Y.2    Koyano, Y.3    Oishi, Y.4
  • 26
    • 48749148224 scopus 로고
    • Rattle: A velocity version of the shake algorithm for molecular dynamics calculations
    • Andersen, H. C. Rattle: A velocity version of the shake algorithm for molecular dynamics calculations J. Comput. Phys. 1983, 52, 24-34
    • (1983) J. Comput. Phys. , vol.52 , pp. 24-34
    • Andersen, H.C.1
  • 27
    • 84870212823 scopus 로고    scopus 로고
    • Maintain rigid structures in Verlet based Cartesian molecular dynamics simulations
    • Tao, P.; Wu, X. W.; Brooks, B. R. Maintain rigid structures in Verlet based Cartesian molecular dynamics simulations J. Chem. Phys. 2012, 137, 134110
    • (2012) J. Chem. Phys. , vol.137 , pp. 134110
    • Tao, P.1    Wu, X.W.2    Brooks, B.R.3
  • 29
    • 84907969132 scopus 로고    scopus 로고
    • Reaction Path Optimization and Sampling Methods and Their Applications for Rare Events
    • Pahlavani, M. R. InTech: Rijeka, Croatia
    • Tao, P.; Larkin, J. D.; Brooks, B. R. Reaction Path Optimization and Sampling Methods and Their Applications for Rare Events. In Some Applications of Quantum Mechanics; Pahlavani, M. R., Ed.; InTech: Rijeka, Croatia, 2012, 27-66.
    • (2012) Some Applications of Quantum Mechanics , pp. 27-66
    • Tao, P.1    Larkin, J.D.2    Brooks, B.R.3
  • 31
    • 77954701668 scopus 로고
    • Classical partition function of a rigid rotator
    • Desloge, E. A. Classical partition function of a rigid rotator Am. J. Phys. 1984, 52, 261-262
    • (1984) Am. J. Phys. , vol.52 , pp. 261-262
    • Desloge, E.A.1
  • 32
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
    • Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method J. Comput. Chem. 1992, 13, 1011-1021
    • (1992) J. Comput. Chem. , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 37
    • 47249122135 scopus 로고    scopus 로고
    • A universal approach to solvation modeling
    • Cramer, C. J.; Truhlar, D. G. A universal approach to solvation modeling Acc. Chem. Res. 2008, 41, 760-768
    • (2008) Acc. Chem. Res. , vol.41 , pp. 760-768
    • Cramer, C.J.1    Truhlar, D.G.2
  • 38
    • 36849121788 scopus 로고
    • Molecular Partition Functions in Terms of Local Properties
    • Herschbach, D. R.; Johnston, H. S.; Rapp, D. Molecular Partition Functions in Terms of Local Properties J. Chem. Phys. 1959, 31, 1652-1661
    • (1959) J. Chem. Phys. , vol.31 , pp. 1652-1661
    • Herschbach, D.R.1    Johnston, H.S.2    Rapp, D.3
  • 39
    • 0000204832 scopus 로고    scopus 로고
    • The Jacobian factor in free energy simulations
    • Boresch, S.; Karplus, M. The Jacobian factor in free energy simulations J. Chem. Phys. 1996, 105, 5145-5154
    • (1996) J. Chem. Phys. , vol.105 , pp. 5145-5154
    • Boresch, S.1    Karplus, M.2
  • 40
    • 0042787283 scopus 로고    scopus 로고
    • The role of bonded terms in free energy simulations: 1. Theoretical analysis
    • Boresch, S.; Karplus, M. The role of bonded terms in free energy simulations: 1. Theoretical analysis J. Phys. Chem. A 1999, 103, 103-118
    • (1999) J. Phys. Chem. A , vol.103 , pp. 103-118
    • Boresch, S.1    Karplus, M.2
  • 41
    • 57349172273 scopus 로고    scopus 로고
    • Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit
    • Woodcock, H. L.; Zheng, W.; Ghysels, A.; Shao, Y.; Kong, J.; Brooks, B. R. Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit J. Chem. Phys. 2008, 129, 214109
    • (2008) J. Chem. Phys. , vol.129 , pp. 214109
    • Woodcock, H.L.1    Zheng, W.2    Ghysels, A.3    Shao, Y.4    Kong, J.5    Brooks, B.R.6
  • 42
    • 84866734974 scopus 로고    scopus 로고
    • Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining
    • Ghysels, A.; Miller, B. T.; Pickard, F. C.; Brooks, B. R. Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining J. Comput. Chem. 2012, 33, 2250-2275
    • (2012) J. Comput. Chem. , vol.33 , pp. 2250-2275
    • Ghysels, A.1    Miller, B.T.2    Pickard, F.C.3    Brooks, B.R.4
  • 43
    • 84908014886 scopus 로고    scopus 로고
    • Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations
    • Submitted for publication.
    • König, G.; Brooks, B. R. Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations. Biochim. Biophys. Acta Submitted for publication.
    • Biochim. Biophys. Acta
    • König, G.1    Brooks, B.R.2
  • 44
    • 36549100582 scopus 로고
    • Treatment of rotational isomers in free energy calculations. II. Molecular dynamics simulation study of 18-crown-6 in aqueous solution as an example of systems with large numbers of rotational isomeric states
    • Straatsma, T. P.; McCammon, J. A. Treatment of rotational isomers in free energy calculations. II. Molecular dynamics simulation study of 18-crown-6 in aqueous solution as an example of systems with large numbers of rotational isomeric states J. Chem. Phys. 1989, 91, 3631-3637
    • (1989) J. Chem. Phys. , vol.91 , pp. 3631-3637
    • Straatsma, T.P.1    McCammon, J.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.