메뉴 건너뛰기




Volumn 9, Issue 2, 2013, Pages 909-926

Simple quantitative tests to validate sampling from thermodynamic ensembles

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84873626426     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct300688p     Document Type: Article
Times cited : (67)

References (27)
  • 1
    • 0001430231 scopus 로고    scopus 로고
    • The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition
    • Harvey, S. C.; Tan, R. K. Z.; Cheatham, T. E. The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition J. Comput. Chem. 1998, 19, 726-740
    • (1998) J. Comput. Chem. , vol.19 , pp. 726-740
    • Harvey, S.C.1    Tan, R.K.Z.2    Cheatham, T.E.3
  • 2
    • 0001538909 scopus 로고
    • Canonical dyanmics: Equilibrium phase-space distributions
    • Hoover, W. G. Canonical dyanmics: Equilibrium phase-space distributions Phys. Rev. A 1985, 31, 1695-1697
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 3
    • 0037305918 scopus 로고    scopus 로고
    • Multiplexed-replica exchange molecular dynamics method for protein folding simulation
    • Rhee, Y. M.; Pande, V. S. Multiplexed Replica Exchange Molecular Dynamics Method for Protein Folding Simulation Biophys. J. 2003, 84, 775-786 (Pubitemid 36133406)
    • (2003) Biophysical Journal , vol.84 , Issue.2 , pp. 775-786
    • Young, M.R.1    Pande, V.S.2
  • 4
    • 38349093284 scopus 로고    scopus 로고
    • Exchange frequency in replica exchange molecular dynamics
    • Sindhikara, D.; Meng, Y.; Roitberg, A. E. Exchange frequency in replica exchange molecular dynamics J. Chem. Phys. 2008, 128, 024103
    • (2008) J. Chem. Phys. , vol.128 , pp. 024103
    • Sindhikara, D.1    Meng, Y.2    Roitberg, A.E.3
  • 5
    • 0242677537 scopus 로고    scopus 로고
    • Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods
    • Shirts, M. R.; Bair, E.; Hooker, G.; Pande, V. S. Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods Phys. Rev. Lett. 2003, 91, 140601
    • (2003) Phys. Rev. Lett. , vol.91 , pp. 140601
    • Shirts, M.R.1    Bair, E.2    Hooker, G.3    Pande, V.S.4
  • 6
    • 83455177868 scopus 로고    scopus 로고
    • A benchmark test set for alchemical free energy transformations and its use to quantify error in common free energy methods
    • Paliwal, H.; Shirts, M. R. A benchmark test set for alchemical free energy transformations and its use to quantify error in common free energy methods J. Chem. Theory Comput. 2011, 7, 4115-4134
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 4115-4134
    • Paliwal, H.1    Shirts, M.R.2
  • 8
    • 0000923503 scopus 로고
    • Asymptotic Theory of Certain "goodness of Fit" Criteria Based on Stochastic Processes
    • Anderson, T. W.; Darling, D. A. Asymptotic Theory of Certain "Goodness of Fit" Criteria Based on Stochastic Processes Ann. Math. Stat. 1952, 23, 193-212
    • (1952) Ann. Math. Stat. , vol.23 , pp. 193-212
    • Anderson, T.W.1    Darling, D.A.2
  • 9
    • 84947138139 scopus 로고
    • Grand Ensemble Monte-Carlo Studies of Physical Adsorption. 1. Results for multilayer adsorption of 12-6 argon in field of a plane homogeneous solid
    • Rowley, L. A.; Nicholson, D.; Parsonage, N. Grand Ensemble Monte-Carlo Studies of Physical Adsorption. 1. Results for multilayer adsorption of 12-6 argon in field of a plane homogeneous solid Mol. Phys. 1976, 31, 365-387
    • (1976) Mol. Phys. , vol.31 , pp. 365-387
    • Rowley, L.A.1    Nicholson, D.2    Parsonage, N.3
  • 10
    • 33846086933 scopus 로고    scopus 로고
    • Canonical sampling through velocity rescaling
    • Bussi, G.; Donadio, D.; Parrinello, M. Canonical sampling through velocity rescaling J. Chem. Phys. 2007, 126, 014101
    • (2007) J. Chem. Phys. , vol.126 , pp. 014101
    • Bussi, G.1    Donadio, D.2    Parrinello, M.3
  • 11
    • 36749107785 scopus 로고
    • Molecular dynamics simulations at constant pressure and/or temperature
    • Andersen, H. C. Molecular dynamics simulations at constant pressure and/or temperature J. Chem. Phys. 1980, 72, 2384-2393
    • (1980) J. Chem. Phys. , vol.72 , pp. 2384-2393
    • Andersen, H.C.1
  • 13
    • 0034702646 scopus 로고    scopus 로고
    • Fluctuation formulas in molecular-dynamics simulations with the weak coupling heat bath
    • Morishita, T. Fluctuation formulas in molecular-dynamics simulations with the weak coupling heat bath J. Chem. Phys. 2000, 113, 2976-2982
    • (2000) J. Chem. Phys. , vol.113 , pp. 2976-2982
    • Morishita, T.1
  • 14
    • 0028697725 scopus 로고    scopus 로고
    • On the Berendsen thermostat
    • S., L. A.; Balabaev, N. K. On the Berendsen thermostat Mol. Simul. 2002, 13, 177-187
    • (2002) Mol. Simul. , vol.13 , pp. 177-187
    • A, S.L.1    Balabaev, N.K.2
  • 15
    • 0040027144 scopus 로고    scopus 로고
    • Dynamic attractor for Berendsen's thermostat and the slow dynamics
    • Golo, V. L.; Shaitan, K. V. Dynamic attractor for Berendsen's thermostat and the slow dynamics Biofizika 2002, 47, 611-617
    • (2002) Biofizika , vol.47 , pp. 611-617
    • Golo, V.L.1    Shaitan, K.V.2
  • 16
    • 52949088587 scopus 로고    scopus 로고
    • Statistically optimal analysis of samples from multiple equilibrium states
    • Shirts, M. R.; Chodera, J. D. Statistically optimal analysis of samples from multiple equilibrium states J. Chem. Phys. 2008, 129, 124105
    • (2008) J. Chem. Phys. , vol.129 , pp. 124105
    • Shirts, M.R.1    Chodera, J.D.2
  • 17
    • 84952104504 scopus 로고
    • An analysis of the accuracy of Langevin and molecular dynamics algorithms
    • Pastor, R. W.; Brooks, B. R.; Szabo, A. An analysis of the accuracy of Langevin and molecular dynamics algorithms Mol. Phys. 1988, 65, 1409-1419
    • (1988) Mol. Phys. , vol.65 , pp. 1409-1419
    • Pastor, R.W.1    Brooks, B.R.2    Szabo, A.3
  • 18
    • 36148997683 scopus 로고    scopus 로고
    • On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm
    • Cuendet, M. A.; van Gunsteren, W. F. On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm J. Chem. Phys. 2007, 127, 184102
    • (2007) J. Chem. Phys. , vol.127 , pp. 184102
    • Cuendet, M.A.1    Van Gunsteren, W.F.2
  • 19
    • 0019707626 scopus 로고
    • Polymorphic transitions in single crystals: A new molecular dynamics method
    • DOI 10.1063/1.328693
    • Parrinello, M.; Rahman, A. Polymorphic transitions in single crystals: A new molecular dynamics method J. Appl. Phys. 1981, 52, 7182-7190 (Pubitemid 12456820)
    • (1981) Journal of Applied Physics , vol.52 , Issue.12 , pp. 7182-7190
    • Parrinello, M.1    Rahman, A.2
  • 20
    • 84926811618 scopus 로고
    • Constant pressure molecular dynamics for molecular systems
    • Nosé, S.; Klein, M. L. Constant pressure molecular dynamics for molecular systems Mol. Phys. 1983, 50, 1055-1076
    • (1983) Mol. Phys. , vol.50 , pp. 1055-1076
    • Nosé, S.1    Klein, M.L.2
  • 21
    • 33646236900 scopus 로고    scopus 로고
    • A Liouville-operator derived measure-preserving integrator for molecular dynamics simulations in the isothermal-isobaric ensemble
    • DOI 10.1088/0305-4470/39/19/S18, PII S0305447006107714
    • Tuckerman, M. E.; Alejandre, J.; López-Rendón, R.; Jochim, A. L.; Martyna, G. J. A Liouville-operator derived measure-preserving integrator for molecular dynamics simulations in the isothermal-isobaric ensemble J. Phys. A 2006, 39, 5629-5651 (Pubitemid 43659105)
    • (2006) Journal of Physics A: Mathematical and General , vol.39 , Issue.19 , pp. 5629-5651
    • Tuckerman, M.E.1    Alejandre, J.2    Lopez-Rendon, R.3    Jochim, A.L.4    Martyna, G.J.5
  • 22
    • 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, 1117-1157 (Pubitemid 126453963)
    • (1996) Molecular Physics , vol.87 , Issue.5 , pp. 1117-1157
    • Martyna, G.J.1    Tuckerman, M.E.2    Tobias, D.J.3    Klein, M.L.4
  • 23
    • 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
  • 24
    • 84986440341 scopus 로고
    • SETTLE: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • Miyamoto, S.; Kollman, P. A. SETTLE: an analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 1992, 13, 952-962
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 25
    • 77956889283 scopus 로고
    • Separate Sample Logistic Discrimination
    • Anderson, J. A. Separate Sample Logistic Discrimination Biometrika 1972, 59, 19-35
    • (1972) Biometrika , vol.59 , pp. 19-35
    • Anderson, J.A.1
  • 26
    • 34247162359 scopus 로고    scopus 로고
    • Non-ergodicity of the Nose-Hoover thermostatted harmonic oscillator
    • Legoll, F.; Luskin, M.; Moeckel, R. Non-ergodicity of the Nose-Hoover thermostatted harmonic oscillator Arch. Rational Mech. Anal. 2007, 184, 449-463
    • (2007) Arch. Rational Mech. Anal. , vol.184 , pp. 449-463
    • Legoll, F.1    Luskin, M.2    Moeckel, R.3
  • 27
    • 67650763419 scopus 로고    scopus 로고
    • Non-ergodicity of Nose-Hoover dynamics
    • Legoll, F.; Luskin, M.; Moeckel, R. Non-ergodicity of Nose-Hoover dynamics Nonlinearity 2009, 22, 1673-1694
    • (2009) Nonlinearity , vol.22 , pp. 1673-1694
    • Legoll, F.1    Luskin, M.2    Moeckel, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.