메뉴 건너뛰기




Volumn 35, Issue 5, 2009, Pages 349-357

Novel procedure for thermal equilibration in molecular dynamics simulation

Author keywords

Molecular dynamics; Solvent coupling; Thermal equilibrium

Indexed keywords

HEAT BATH; HEURISTIC APPROACH; KEY ELEMENTS; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; NON EQUILIBRIUM; PRINCIPAL COMPONENTS ANALYSIS; ROOT-MEAN SQUARE DEVIATION; SIMULATION TIME; THERMAL EQUILIBRATIONS; THERMAL EQUILIBRIUM; THERMAL EQUILIBRIUMS;

EID: 70449580785     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020802647272     Document Type: Article
Times cited : (8)

References (28)
  • 1
    • 0018791973 scopus 로고
    • Dynamics of ligand binding to heme proteins
    • D.A. Case and M. Karplus, Dynamics of ligand binding to heme proteins, J. Mol. Biol. 132 (1979), pp. 343-368.
    • (1979) J. Mol. Biol. , vol.132 , pp. 343-368
    • Case, D.A.1    Karplus, M.2
  • 2
    • 0024354001 scopus 로고
    • Solvent effects on protein motion and protein effects on solvent motion dynamics of the active site region of lysozyme
    • C.L. Brooks and M. Karplus, Solvent effects on protein motion and protein effects on solvent motion dynamics of the active site region of lysozyme, J. Mol. Biol. 208 (1989), pp. 159-181.
    • (1989) J. Mol. Biol. , vol.208 , pp. 159-181
    • Brooks, C.L.1    Karplus, M.2
  • 3
    • 0025015392 scopus 로고
    • Anatomy of a conformational change: Hinged 'lid' motion of the triosephosphate isomerase loop
    • D. Joseph, G.A. Petsko, and M. Karplus, Anatomy of a conformational change: hinged 'lid' motion of the triosephosphate isomerase loop, Science 249 (1990), pp. 1425-1428.
    • (1990) Science , vol.249 , pp. 1425-1428
    • Joseph, D.1    Petsko, G.A.2    Karplus, M.3
  • 4
    • 0024103632 scopus 로고
    • Dynamic simulation as an essential tool in molecular modeling
    • H.J. Berendsen, Dynamic simulation as an essential tool in molecular modeling, J. Comput. Aided Mol. Des. 2 (1988), pp. 217-221.
    • (1988) J. Comput. Aided Mol. Des. , vol.2 , pp. 217-221
    • Berendsen, H.J.1
  • 9
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • M. Karplus and J.A. McCammon, Molecular dynamics simulations of biomolecules, Nature Struc. Biol. 9 (2002), pp. 646-665.
    • (2002) Nature Struc. Biol. , vol.9 , pp. 646-665
    • Karplus, M.1    McCammon, J.A.2
  • 10
    • 34547809547 scopus 로고
    • A unified formulation of the constant temperature molecular dynamics methods
    • S.J. Nose, A unified formulation of the constant temperature molecular dynamics methods, Chem. Phys. 81 (1984), pp. 511-519.
    • (1984) Chem. Phys. , vol.81 , pp. 511-519
    • Nose, S.J.1
  • 11
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • W.G. Hoover, Canonical dynamics: Equilibrium phase-space distributions, Phys. Rev. A 31 (1985), pp. 1695-1697.
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 13
    • 33745714406 scopus 로고    scopus 로고
    • Mechanism of titin unfolding by force: Insight from quasi-equilibrium molecular dynamics calculations
    • G. Pabón and L.M. Amzel, Mechanism of titin unfolding by force: insight from quasi-equilibrium molecular dynamics calculations, Biophys. J. 91 (2006), pp. 467-472.
    • (2006) Biophys. J. , vol.91 , pp. 467-472
    • Pabón, G.1    Amzel, L.M.2
  • 17
    • 0028887396 scopus 로고
    • Full matrix refinement of the protein crambin at 083A ° and 130K
    • B. Stec, R.S. Zhou, and M.M. Teeter, Full matrix refinement of the protein crambin at 083A ° and 130K, Acta Cryst. D 51 (1995), pp. 663-681.
    • (1995) Acta Cryst. D , vol.51 , pp. 663-681
    • Stec, B.1    Zhou, R.S.2    Teeter, M.M.3
  • 18
    • 0030938277 scopus 로고    scopus 로고
    • Crystal structure of Kringle 4 at 168A ° resolution and 48C a possible structural role of disordered residues
    • B. Stec, A. Yamano, M. Whitlow, and M.M. Teeter, Crystal structure of Kringle 4 at 168A ° resolution and 48C a possible structural role of disordered residues, Acta Cryst. D 53 (1997), pp. 169-178.
    • (1997) Acta Cryst. D , vol.53 , pp. 169-178
    • Stec, B.1    Yamano, A.2    Whitlow, M.3    Teeter, M.M.4
  • 19
    • 0000094135 scopus 로고    scopus 로고
    • Collective motion artifacts arising in long-duration molecular dynamics
    • S.W. Chiu, M. Clark, S. Subramaniam, and E. Jakobsson, Collective motion artifacts arising in long-duration molecular dynamics, J. Comp. Chem. 21 (2000), pp. 121-131.
    • (2000) J. Comp. Chem. , vol.21 , pp. 121-131
    • Chiu, S.W.1    Clark, M.2    Subramaniam, S.3    Jakobsson, E.4
  • 20
    • 0001430231 scopus 로고    scopus 로고
    • The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition
    • S.C. Harvey, R.K.-Z. Tan, and T.E. Cheatham III, The flying ice cube: velocity rescaling in molecular dynamics leads to violation of energy equipartition, J. Comp. Chem. 19 (1998), pp. 726-740.
    • (1998) J. Comp. Chem. , vol.19 , pp. 726-740
    • Harvey, S.C.1    Tan, R.K.-Z.2    Cheatham Iii, T.E.3
  • 22
    • 0034295613 scopus 로고    scopus 로고
    • Macroscopic expressions for the thermodynamic temperature
    • O.G. Jepps, G. Ayton, and D.J. Evans, Macroscopic expressions for the thermodynamic temperature, Phys. Rev. E 62 (2000), pp. 4757-4763.
    • (2000) Phys. Rev. e , vol.62 , pp. 4757-4763
    • Jepps, O.G.1    Ayton, G.2    Evans, D.J.3
  • 23
    • 22244491267 scopus 로고    scopus 로고
    • Configurational temperature: Verification of Monte Carlo simulations
    • B.D. Butler, G. Ayton, O.G. Jepps, and D.J. Evans, Configurational temperature: verification of Monte Carlo simulations, J. Chem. Phys. 109 (1998), pp. 6519-6522.
    • (1998) J. Chem. Phys. , vol.109 , pp. 6519-6522
    • Butler, B.D.1    Ayton, G.2    Jepps, O.G.3    Evans, D.J.4
  • 24
    • 0001112302 scopus 로고    scopus 로고
    • Dynamical approach to temperature
    • H.H. Rugh, Dynamical approach to temperature, Phys. Rev. Lett. 78 (1997), pp. 772-774.
    • (1997) Phys. Rev. Lett. , vol.78 , pp. 772-774
    • Rugh, H.H.1
  • 25
    • 0035396367 scopus 로고    scopus 로고
    • Comparison of thermostatting mechanisms in NVT and NPT simulations of decane under shear
    • J. Delhommelle and D.J. Evans, Comparison of thermostatting mechanisms in NVT and NPT simulations of decane under shear, J. Chem. Phys. 115 (2001), pp. 43-49.
    • (2001) J. Chem. Phys. , vol.115 , pp. 43-49
    • Delhommelle, J.1    Evans, D.J.2
  • 26
    • 34547555011 scopus 로고    scopus 로고
    • Shear thickening in a model colloidal suspension
    • J. Delhommelle and J. Petravic, Shear thickening in a model colloidal suspension, J. Chem. Phys. 123 (2005), 074707-1-074707-74715
    • (2005) J. Chem. Phys. , vol.123
    • Delhommelle, J.1    Petravic, J.2
  • 27
    • 0344118922 scopus 로고    scopus 로고
    • Configurational temperature density of states simulations of proteins
    • N. Rathore, T.A. Knotts IV, and J.J. de Pablo, Configurational temperature density of states simulations of proteins, J. Chem. Phys. 85 (2003), pp. 3963-3968.
    • (2003) J. Chem. Phys. , vol.85 , pp. 3963-3968
    • Rathore, N.1    Knotts Iv, T.A.2    Pablo De, J.J.3
  • 28
    • 2542444786 scopus 로고    scopus 로고
    • Configurational temperature of chargestabilized colloidal monolayers
    • Y. Han and D.G. Grier, Configurational temperature of chargestabilized colloidal monolayers, Phys. Rev. Lett. 92 (2004), 148301-1-148301-148305
    • (2004) Phys. Rev. Lett. , vol.92
    • Han, Y.1    Grier, D.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.