메뉴 건너뛰기




Volumn 119, Issue 3, 2015, Pages 736-742

A time-independent free energy estimator for metadynamics

Author keywords

[No Author keywords available]

Indexed keywords

PHYSICAL CHEMISTRY;

EID: 84907327659     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp504920s     Document Type: Article
Times cited : (435)

References (27)
  • 1
    • 0036424048 scopus 로고    scopus 로고
    • 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
    • (2002) Annu. Rev. Phys. Chem. , vol.53 , pp. 291-318
    • Bolhuis, P.G.1    Chandler, D.2    Dellago, C.3    Geissler, P.L.4
  • 3
    • 0036040917 scopus 로고    scopus 로고
    • Extending the Time Scale in Atomistic Simulation of Materials
    • Voter, A. F.; Montalenti, F.; Germann, T. C. Extending the Time Scale in Atomistic Simulation of Materials Annu. Rev. Mater. Res. 2002, 32, 321-346
    • (2002) Annu. Rev. Mater. Res. , vol.32 , pp. 321-346
    • Voter, A.F.1    Montalenti, F.2    Germann, T.C.3
  • 5
    • 0028710015 scopus 로고
    • Local elevation: A Method for Improving the Searching Properties of Molecular Dynamics Simulation
    • Huber, T.; Torda, A.; van Gunsteren, W. Local elevation: A Method for Improving the Searching Properties of Molecular Dynamics Simulation J. Comput. Mol. Des. 1994, 8, 695-708
    • (1994) J. Comput. Mol. Des. , vol.8 , pp. 695-708
    • Huber, T.1    Torda, A.2    Van Gunsteren, W.3
  • 6
    • 0000689085 scopus 로고
    • Predicting Slow Structural Transitions in Macromolecular Systems: Conformational Flooding
    • Grubmüller, H. Predicting Slow Structural Transitions in Macromolecular Systems: Conformational Flooding Phys. Rev. E 1995, 52, 2893-2906
    • (1995) Phys. Rev. e , vol.52 , pp. 2893-2906
    • Grubmüller, H.1
  • 7
    • 1442281293 scopus 로고    scopus 로고
    • 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
    • (1997) J. Chem. Phys. , vol.106 , pp. 4665-4677
    • Voter, A.F.1
  • 8
    • 80053577091 scopus 로고    scopus 로고
    • Hybrid Deterministic and Stochastic Approach for Efficient Atomistic Simulations at Long Time Scales
    • Tiwary, P.; van de Walle, A. Hybrid Deterministic and Stochastic Approach for Efficient Atomistic Simulations at Long Time Scales Phys. Rev. B 2011, 84, 100301-100304
    • (2011) Phys. Rev. B , vol.84 , pp. 100301-100304
    • Tiwary, P.1    Van De Walle, A.2
  • 9
    • 80055023346 scopus 로고    scopus 로고
    • Multiple State Transition Interface Sampling of Alanine Dipeptide in Explicit Solvent
    • Du, W.-N.; Marino, K. A.; Bolhuis, P. G. Multiple State Transition Interface Sampling of Alanine Dipeptide in Explicit Solvent J. Chem. Phys. 2011, 135, 145102-145108
    • (2011) J. Chem. Phys. , vol.135 , pp. 145102-145108
    • Du, W.-N.1    Marino, K.A.2    Bolhuis, P.G.3
  • 10
    • 0001299795 scopus 로고    scopus 로고
    • Simple Bias Potential for Boosting Molecular Dynamics with the Hyperdynamics Scheme
    • Steiner, M. M.; Genilloud, P.-A.; Wilkins, J. W. Simple Bias Potential for Boosting Molecular Dynamics with the Hyperdynamics Scheme Phys. Rev. B 1998, 57, 10236-10239
    • (1998) Phys. Rev. B , vol.57 , pp. 10236-10239
    • Steiner, M.M.1    Genilloud, P.-A.2    Wilkins, J.W.3
  • 11
    • 84875322422 scopus 로고    scopus 로고
    • 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 2013, 87, 094304-094310
    • (2013) Phys. Rev. B , vol.87 , pp. 094304-094310
    • Tiwary, P.1    Van De Walle, A.2
  • 12
    • 84902817448 scopus 로고    scopus 로고
    • A Well-Tempered Metadynamics Converges Asymptotically
    • Dama, J. F.; Parrinello, M.; Voth, G. A. A Well-Tempered Metadynamics Converges Asymptotically Phys. Rev. Lett. 2014, 112, 240602-240608
    • (2014) Phys. Rev. Lett. , vol.112 , pp. 240602-240608
    • Dama, J.F.1    Parrinello, M.2    Voth, G.A.3
  • 13
    • 38349091489 scopus 로고    scopus 로고
    • 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, 020603-020606
    • (2008) Phys. Rev. Lett. , vol.100 , pp. 020603-020606
    • Barducci, A.1    Bussi, G.2    Parrinello, M.3
  • 14
    • 33644772083 scopus 로고    scopus 로고
    • Equilibrium Free Energies from Nonequilibrium Metadynamics
    • Bussi, G.; Laio, A.; Parrinello, M. Equilibrium Free Energies from Nonequilibrium Metadynamics Phys. Rev. Lett. 2006, 96, 090601-090604
    • (2006) Phys. Rev. Lett. , vol.96 , pp. 090601-090604
    • Bussi, G.1    Laio, A.2    Parrinello, M.3
  • 15
    • 77952354685 scopus 로고    scopus 로고
    • Metadynamics Convergence Law in a Multidimensional System
    • Crespo, Y.; Marinelli, F.; Pietrucci, F.; Laio, A. Metadynamics Convergence Law in a Multidimensional System Phys. Rev. E 2010, 81, 055701-055704
    • (2010) Phys. Rev. e , vol.81 , pp. 055701-055704
    • Crespo, Y.1    Marinelli, F.2    Pietrucci, F.3    Laio, A.4
  • 16
    • 67650477115 scopus 로고    scopus 로고
    • Reconstructing the Equilibrium Boltzmann Distribution fromWell-tempered Metadynamics
    • Bonomi, M.; Barducci, A.; Parrinello, M. Reconstructing the Equilibrium Boltzmann Distribution fromWell-tempered Metadynamics J. Comput. Chem. 2009, 30, 1615-1621
    • (2009) J. Comput. Chem. , vol.30 , pp. 1615-1621
    • Bonomi, M.1    Barducci, A.2    Parrinello, M.3
  • 18
    • 45849125004 scopus 로고    scopus 로고
    • Estimation of Microscopic Averages from Metadynamics
    • Tiana, G. Estimation of Microscopic Averages from Metadynamics Eur. Phys. J. B 2008, 63, 235-238
    • (2008) Eur. Phys. J. B , vol.63 , pp. 235-238
    • Tiana, G.1
  • 19
    • 79958192770 scopus 로고    scopus 로고
    • Calculation of Free Energy Landscapes: A Histogram Reweighted Metadynamics Approach
    • Smiatek, J.; Heuer, A. Calculation of Free Energy Landscapes: A Histogram Reweighted Metadynamics Approach J. Comput. Chem. 2011, 32, 2084-2096
    • (2011) J. Comput. Chem. , vol.32 , pp. 2084-2096
    • Smiatek, J.1    Heuer, A.2
  • 20
    • 84889779905 scopus 로고    scopus 로고
    • From Metadynamics to Dynamics
    • Tiwary, P.; Parrinello, M. From Metadynamics to Dynamics Phys. Rev. Lett. 2013, 111, 230602-230606
    • (2013) Phys. Rev. Lett. , vol.111 , pp. 230602-230606
    • Tiwary, P.1    Parrinello, M.2
  • 21
    • 84898429568 scopus 로고    scopus 로고
    • 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, 1420-1425
    • (2014) J. Chem. Theory Comput. , pp. 1420-1425
    • Salvalaglio, M.1    Tiwary, P.2    Parrinello, M.3
  • 22
    • 23444454552 scopus 로고    scopus 로고
    • The Amber Biomolecular Simulation Programs
    • Case, D. A.; Cheatham, T. E.; Darden, T. The Amber Biomolecular Simulation Programs J. Comput. Chem. 2005, 26, 1668-1688
    • (2005) J. Comput. Chem. , vol.26 , pp. 1668-1688
    • Case, D.A.1    Cheatham, T.E.2    Darden, T.3
  • 23
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A Package for Molecular Simulation and Trajectory Analysis
    • Lindahl, E.; Hess, B.; Van Der Spoel, D. GROMACS 3.0: a Package for Molecular Simulation and Trajectory Analysis J. Mol. Model. 2001, 7, 306-317
    • (2001) J. Mol. Model. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 24
    • 69349100797 scopus 로고    scopus 로고
    • PLUMED: A Portable Plugin for Freeenergy Calculations with Molecular Dynamics
    • Bonomi, M.; Branduardi, D.; Bussi, G. PLUMED: A Portable Plugin for Freeenergy Calculations with Molecular Dynamics Comp. Phys. Comm. 2009, 180, 1961-1972
    • (2009) Comp. Phys. Comm. , vol.180 , pp. 1961-1972
    • Bonomi, M.1    Branduardi, D.2    Bussi, G.3
  • 25
    • 0000388705 scopus 로고    scopus 로고
    • LINCS: A Linear Constraint Solver for Molecular Simulations
    • Hess, B.; Bekker, H.; Berendsen, H. J.; Fraaije, J. G. LINCS: a Linear Constraint Solver for Molecular Simulations J. Comput. Chem. 1997, 18, 1463-1472
    • (1997) J. Comput. Chem. , vol.18 , pp. 1463-1472
    • Hess, B.1    Bekker, H.2    Berendsen, H.J.3    Fraaije, J.G.4
  • 26
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An Nlog (N) method for Ewald sums in large systems
    • Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An Nlog (N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 27


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.