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Volumn 10, Issue 12, 2014, Pages 5276-5285

Multiple-replica strategies for free-energy calculations in NAMD: Multiple-walker adaptive biasing force and walker selection rules

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EID: 84916210744     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct500874p     Document Type: Article
Times cited : (74)

References (41)
  • 3
    • 84890794190 scopus 로고    scopus 로고
    • Frontiers in Free-Energy Calculations of Biological Systems
    • Chipot, C. Frontiers in Free-Energy Calculations of Biological Systems. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2014, 4, 71-89.
    • (2014) Wiley Interdiscip. Rev. Comput. Mol. Sci. , vol.4 , pp. 71-89
    • Chipot, C.1
  • 4
    • 84872165531 scopus 로고    scopus 로고
    • Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
    • Gumbart, J. C.; Roux, B.; Chipot, C. Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy? J. Chem. Theory Comput. 2012, 9, 794-802.
    • (2012) J. Chem. Theory Comput. , vol.9 , pp. 794-802
    • Gumbart, J.C.1    Roux, B.2    Chipot, C.3
  • 6
    • 18744387720 scopus 로고    scopus 로고
    • Reaction Coordinates and Rates from Transition Paths
    • Best, R.; Hummer, G. Reaction Coordinates and Rates from Transition Paths. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6732.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 6732
    • Best, R.1    Hummer, G.2
  • 7
    • 34848923636 scopus 로고    scopus 로고
    • Energetics of Ion Transport in a Peptide Nanotube
    • Dehez, F.; Tarek, M.; Chipot, C. Energetics of Ion Transport in a Peptide Nanotube. J. Phys. Chem. B 2007, 111, 10633-10635.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 10633-10635
    • Dehez, F.1    Tarek, M.2    Chipot, C.3
  • 8
    • 77950102787 scopus 로고    scopus 로고
    • Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables
    • Hénin, J.; Fiorin, G.; Chipot, C.; Klein, M. Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables. J. Chem. Theory Comput. 2009, 6, 35-47.
    • (2009) J. Chem. Theory Comput. , vol.6 , pp. 35-47
    • Hénin, J.1    Fiorin, G.2    Chipot, C.3    Klein, M.4
  • 9
    • 84898897801 scopus 로고    scopus 로고
    • Unknown Unknowns: The Challenge of Systematic and Statistical Error in Molecular Dynamics Simulations
    • Romo, T. D.; Grossfield, A. Unknown Unknowns: The Challenge of Systematic and Statistical Error in Molecular Dynamics Simulations. Biophys. J. 2014, 106, 1553-1554.
    • (2014) Biophys. J. , vol.106 , pp. 1553-1554
    • Romo, T.D.1    Grossfield, A.2
  • 10
    • 58149512801 scopus 로고    scopus 로고
    • Random Walk in Orthogonal Space to Achieve Efficient Free-energy Simulation of Complex Systems
    • Zheng, L.; Chen, M.; Yang, W. Random Walk in Orthogonal Space to Achieve Efficient Free-energy Simulation of Complex Systems. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 20227-20232.
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 20227-20232
    • Zheng, L.1    Chen, M.2    Yang, W.3
  • 12
    • 67649114369 scopus 로고    scopus 로고
    • Simultaneous Escaping of Explicit and Hidden Free Energy Barriers: Application of the Orthogonal Space Random Walk Strategy in Generalized Ensemble Based Conformational Sampling
    • Zheng, L.; Chen, M.; Yang, W. Simultaneous Escaping of Explicit and Hidden Free Energy Barriers: Application of the Orthogonal Space Random Walk Strategy in Generalized Ensemble Based Conformational Sampling. J. Chem. Phys. 2009, 130, 234105.
    • (2009) J. Chem. Phys. , vol.130 , pp. 234105
    • Zheng, L.1    Chen, M.2    Yang, W.3
  • 13
    • 84863366516 scopus 로고    scopus 로고
    • Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering
    • Zheng, L.; Yang, W. Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering. J. Chem. Theory Comput. 2012, 8, 810-823.
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 810-823
    • Zheng, L.1    Yang, W.2
  • 14
    • 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, 141-151.
    • (1999) Chem. Phys. Lett. , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 15
    • 0034294024 scopus 로고    scopus 로고
    • Multidimensional Replica-Exchange Method for Free-Energy Calculations
    • Sugita, Y.; Kitao, A.; Okamoto, Y. Multidimensional Replica-Exchange Method for Free-Energy Calculations. J. Chem. Phys. 2000, 113, 6042-6051.
    • (2000) J. Chem. Phys. , vol.113 , pp. 6042-6051
    • Sugita, Y.1    Kitao, A.2    Okamoto, Y.3
  • 16
    • 0346350789 scopus 로고    scopus 로고
    • The Development of Replica-Exchange-Based Free-Energy Methods
    • Woods, C. J.; Essex, J. W.; King, M. A. The Development of Replica-Exchange-Based Free-Energy Methods. J. Phys. Chem. B 2003, 107, 13703-13710.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 13703-13710
    • Woods, C.J.1    Essex, J.W.2    King, M.A.3
  • 17
    • 41849093720 scopus 로고    scopus 로고
    • Adaptively Biased Molecular Dynamics for Free Energy Calculations
    • Babin, V.; Roland, C.; Sagui, C. Adaptively Biased Molecular Dynamics for Free Energy Calculations. J. Chem. Phys. 2008, 128, 134101.
    • (2008) J. Chem. Phys. , vol.128 , pp. 134101
    • Babin, V.1    Roland, C.2    Sagui, C.3
  • 18
    • 34547314279 scopus 로고    scopus 로고
    • Characterization of Conformational Equilibria through Hamiltonian and Temperature Replica-Exchange Simulations: Assessing Entropic and Environmental Effects
    • Faraldo-Gómez, J. D.; Roux, B. Characterization of Conformational Equilibria through Hamiltonian and Temperature Replica-Exchange Simulations: Assessing Entropic and Environmental Effects. J. Comput. Chem. 2007, 28, 1634-1647.
    • (2007) J. Comput. Chem. , vol.28 , pp. 1634-1647
    • Faraldo-Gómez, J.D.1    Roux, B.2
  • 19
    • 67650498345 scopus 로고    scopus 로고
    • Using Multistate Free Energy Techniques to Improve the Efficiency of Replica Exchange Accelerated Molecular Dynamics
    • Fajer, M.; Swift, R. V.; McCammon, J. A. Using Multistate Free Energy Techniques to Improve the Efficiency of Replica Exchange Accelerated Molecular Dynamics. J. Comput. Chem. 2009, 30, 1719-1725.
    • (2009) J. Comput. Chem. , vol.30 , pp. 1719-1725
    • Fajer, M.1    Swift, R.V.2    McCammon, J.A.3
  • 20
    • 77956574437 scopus 로고    scopus 로고
    • Free Energy Perturbation Hamiltonian Replica-exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations
    • Jiang, W.; Roux, B. Free Energy Perturbation Hamiltonian Replica-exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations. J. Chem. Theory Comput. 2010, 6, 2559-2565.
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 2559-2565
    • Jiang, W.1    Roux, B.2
  • 21
    • 77951140202 scopus 로고    scopus 로고
    • Potential of Mean Force Calculations: A Multiple-walker Adaptive Biasing Force Approach
    • Minoukadeh, K.; Chipot, C.; Lelièvre, T. Potential of Mean Force Calculations: A Multiple-walker Adaptive Biasing Force Approach. J. Chem. Theory Comput. 2010, 6, 1008-1017.
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 1008-1017
    • Minoukadeh, K.1    Chipot, C.2    Lelièvre, T.3
  • 22
    • 84896773262 scopus 로고    scopus 로고
    • Achieving Ergodic Sampling Using Replica-Exchange Free-Energy Calculations
    • Comer, J.; Roux, B.; Chipot, C. Achieving Ergodic Sampling Using Replica-Exchange Free-Energy Calculations. Mol. Sim. 2014, 40, 218-228.
    • (2014) Mol. Sim. , vol.40 , pp. 218-228
    • Comer, J.1    Roux, B.2    Chipot, C.3
  • 24
    • 35949020425 scopus 로고
    • Replica Monte Carlo Simulation of Spin Glasses
    • Swendsen, R. H.; Wang, J.-S. Replica Monte Carlo Simulation of Spin Glasses. Phys. Rev. Lett. 1986, 57, 2607-2609.
    • (1986) Phys. Rev. Lett. , vol.57 , pp. 2607-2609
    • Swendsen, R.H.1    Wang, J.-S.2
  • 25
    • 33644899039 scopus 로고
    • Simulated Tempering: A New Monte Carlo Scheme
    • Marinari, E.; Parisi, G. Simulated Tempering: A New Monte Carlo Scheme. Europhys. Lett. 1992, 19, 451.
    • (1992) Europhys. Lett. , vol.19 , pp. 451
    • Marinari, E.1    Parisi, G.2
  • 26
    • 84953648015 scopus 로고
    • New Approach to Monte Carlo Calculation of the Free Energy: Method of Expanded Ensembles
    • Lyubartsev, A.; Martsinovski, A.; Shevkunov, S.; Vorontsov-Velyaminov, P. New Approach to Monte Carlo Calculation of the Free Energy: Method of Expanded Ensembles. J. Chem. Phys. 1992, 96, 1776-1783.
    • (1992) J. Chem. Phys. , vol.96 , pp. 1776-1783
    • Lyubartsev, A.1    Martsinovski, A.2    Shevkunov, S.3    Vorontsov-Velyaminov, P.4
  • 27
    • 0035935802 scopus 로고    scopus 로고
    • 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
  • 28
    • 4344660645 scopus 로고    scopus 로고
    • Overcoming Free Energy Barriers Using Unconstrained Molecular Dynamics Simulations
    • Hénin, J.; Chipot, C. Overcoming Free Energy Barriers Using Unconstrained Molecular Dynamics Simulations. J. Chem. Phys. 2004, 121, 2904-2914.
    • (2004) J. Chem. Phys. , vol.121 , pp. 2904-2914
    • Hénin, J.1    Chipot, C.2
  • 29
    • 1642617408 scopus 로고    scopus 로고
    • Assessing the Efficiency of Free Energy Calculation Methods
    • Rodriguez-Gomez, D.; Darve, E.; Pohorille, A. Assessing the Efficiency of Free Energy Calculation Methods. J. Chem. Phys. 2004, 120, 3563.
    • (2004) J. Chem. Phys. , vol.120 , pp. 3563
    • Rodriguez-Gomez, D.1    Darve, E.2    Pohorille, A.3
  • 30
    • 45149117115 scopus 로고    scopus 로고
    • Long-time Convergence of an Adaptive Biasing Force Method
    • Lelièvre, T.; Rousset, M.; Stoltz, G. Long-time Convergence of an Adaptive Biasing Force Method. Nonlinearity 2008, 21, 1155.
    • (2008) Nonlinearity , vol.21 , pp. 1155
    • Lelièvre, T.1    Rousset, M.2    Stoltz, G.3
  • 31
    • 79955512132 scopus 로고    scopus 로고
    • Long-time Convergence of an Adaptive Biasing Force Method: The Bi-channel Case
    • Lelievre, T.; Minoukadeh, K. Long-time Convergence of an Adaptive Biasing Force Method: The Bi-channel Case. Archive for Rational Mechanics and Analysis 2011, 202, 1-34.
    • (2011) Archive for Rational Mechanics and Analysis , vol.202 , pp. 1-34
    • Lelievre, T.1    Minoukadeh, K.2
  • 32
    • 34147094596 scopus 로고    scopus 로고
    • Computation of Free Energy Profiles with Parallel Adaptive Dynamics
    • Lelièvre, T.; Rousset, M.; Stoltz, G. Computation of Free Energy Profiles with Parallel Adaptive Dynamics. J. Chem. Phys. 2007, 126, 134111.
    • (2007) J. Chem. Phys. , vol.126 , pp. 134111
    • Lelièvre, T.1    Rousset, M.2    Stoltz, G.3
  • 34
    • 84889585833 scopus 로고    scopus 로고
    • Using Collective Variables to Drive Molecular Dynamics Simulations
    • Fiorin, G.; Klein, M. L.; Hénin, J. Using Collective Variables to Drive Molecular Dynamics Simulations. Mol. Phys. 2013, 111, 3345-3362.
    • (2013) Mol. Phys. , vol.111 , pp. 3345-3362
    • Fiorin, G.1    Klein, M.L.2    Hénin, J.3
  • 36
    • 0043268848 scopus 로고    scopus 로고
    • Reaction Paths Based on Mean First-Passage Times
    • Park, S.; Şener, M. K.; Lu, D.; Schulten, K. Reaction Paths Based on Mean First-Passage Times. J. Chem. Phys. 2003, 119, 1313-1319.
    • (2003) J. Chem. Phys. , vol.119 , pp. 1313-1319
    • Park, S.1    Şener, M.K.2    Lu, D.3    Schulten, K.4
  • 38
    • 1642576012 scopus 로고    scopus 로고
    • Improved Treatment of the Protein Backbone in Empirical Force Fields
    • MacKerell, A., Jr.; Feig, M.; Brooks, C., III Improved Treatment of the Protein Backbone in Empirical Force Fields. J. Am. Chem. Soc. 2004, 126, 698-699.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 698-699
    • MacKerell, A.1    Feig, M.2    Brooks, C.3
  • 39
    • 48749137581 scopus 로고
    • Stochastic Boundary Conditions for Molecular Dynamics Simulations of ST2 Water
    • Brünger, A. T.; Brooks, C. L., III; Karplus, M. Stochastic Boundary Conditions for Molecular Dynamics Simulations of ST2 Water. Chem. Phys. Lett. 1984, 105, 495-498.
    • (1984) Chem. Phys. Lett. , vol.105 , pp. 495-498
    • Brünger, A.T.1    Brooks, C.L.2    Karplus, M.3
  • 40
    • 48749148224 scopus 로고
    • Rattle: A "Velocity" Version of the Shake Algorithm for Molecular Dynamics Calculations
    • Andersen, H. 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.1
  • 41
    • 84904136270 scopus 로고    scopus 로고
    • Thermodynamics of Deca-alanine Folding in Water
    • Hazel, A.; Chipot, C.; Gumbart, J. C. Thermodynamics of Deca-alanine Folding in Water. J. Chem. Theory Comput. 2014, 10, 2836-2844.
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 2836-2844
    • Hazel, A.1    Chipot, C.2    Gumbart, J.C.3


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