Replica-exchange molecular dynamics simulation of a lipid bilayer system with a coarse-grained model

Molecular Simulation

Volumn 38, Issue 5, 2012, Pages 437-441

  Nagai, Tetsuro ^a   Okamoto, Yuko ^a  

^a NAGOYA UNIVERSITY   (Japan)

Author keywords

coarse grained model MARTINI; dipalmitoylphosphatidylcholine (DPPC); lipid bilayer; replica exchange molecular dynamics (REMD) simulation; sol gel phase transition

Indexed keywords

ATOMISTIC MODELS; BI-LAYER; BILAYER SYSTEMS; COARSE GRAINED MODELS; DIPALMITOYL PHOSPHATIDYLCHOLINE; ENERGY LANDSCAPE; FORCE FIELDS; GEL STATE; INTERNAL ENERGIES; REPLICA-EXCHANGE MOLECULAR DYNAMICS (REMD) SIMULATION; REPLICA-EXCHANGE MOLECULAR DYNAMICS SIMULATIONS; SAMPLING EFFICIENCY; SOL-GEL PHASE TRANSITION; TEMPERATURE RANGE; TIME-SCALES; TWO-STATE;

LIPID BILAYERS; MOLECULAR DYNAMICS; PHASE TRANSITIONS;

COMPUTER SIMULATION;

EID: 84859200266     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927022.2011.564172     Document Type: Conference Paper

References (22)

1. A. de Vries, S. Yefimov, A. Mark, and S. Marrink, Molecular structure of the lecithin ripple phase, Proc. National Acad. Sci. USA 102 (2005), pp. 5392-5396.
2. S. Leekumjorn and A. Sum, Molecular studies of the gel to liquidcrystalline phase transition for fully hydrated DPPC and DPPE bilayers, BBA-Biomembr. 1768 (2007), pp. 354-365.
3. S. Leekumjorn and A. Sum, Molecular characterization of gel and liquid-crystalline structures of fully hydrated POPC and POPE bilayers, J. Phys. Chem. B 111 (2007), pp. 6026-6033.
4. S. Marrink, J. Risselada, and A. Mark, Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model, Chem. Phys. Lipids 135 (2005), pp. 223-244.
5. S. Marrink, A. de Vries, and A. Mark, Coarse grained model for semiquantitative lipid simulations, J. Phys. Chem. B 108 (2004), pp. 750-760.
6. S. Marrink, H. Risselada, S. Yefimov, D. Tieleman, and A. de Vries, The MARTINI force field: Coarse grained model for biomolecular simulations, J. Phys. Chem. B-Condens. Phase 111 (2007), pp. 7812-7824.
7. M. Stevens, Coarse-grained simulations of lipid bilayers, J. Chem. Phys. 121 (2004), pp. 11942-11948.
8. Y. Sugita and Y. Okamoto, Replica-exchange molecular dynamics method for protein folding, Chem. Phys. Lett. 314 (1999), pp. 141-151.
9. K. Hukushima and K. Nemoto, Exchange Monte Carlo method and application to spin glass simulations, J. Phys. Soc. Japan 65 (1996), pp. 1604-1608.
10. U. Hansmann and Y. Okamoto, The generalized-ensemble approach for protein folding simulations, in Annual Reviews of Computational Physics VI, D. Stauffer, ed., World Scientific, Singapore, 1999, pp. 129-157.
11. A. Mitsutake, Y. Sugita, and Y. Okamoto, Generalized-ensemble algorithms for molecular simulations of biopolymers, Biopolymers 60 (2001), pp. 96-123.
12. N. Metropolis, A. Rosenbluth, M. Rosenbluth, A. Teller, and E. Teller, Equation of state calculations by fast computing machines, J. Chem. Phys. 21 (1953), pp. 1087-1092.
13. T. Nishikawa, H. Ohtsuka, Y. Sugita, M. Mikami, and Y. Okamoto, Replica-exchange Monte Carlo method for Ar fluid, Prog. Theor. Phys. Suppl. 138 (2000), pp. 270-271.
14. T. Okabe, M. Kawata, Y. Okamoto, and M. Mikami, Replicaexchange Monte Carlo method for the isobaric-isothermal ensemble, Chem. Phys. Lett. 335 (2001), pp. 435-439.
15. Y. Sugita and Y. Okamoto, Free-energy calculations in protein folding by generalized-ensemble algorithms, in Lecture Notes in Computational Science and Engineering, T. Schlick, and H.H. Gan, eds., Springer, Berlin, 2002, pp. 303-331.
16. S. Nosé, A molecular-dynamics method for simulations in the canonical ensemble, Mol. Phys. 52 (1984), pp. 255-268.
17. W. Hoover, Canonical dynamics -Equilibrium phase-space distributions, Phys. Rev. A 31 (1985), pp. 1695-1697.
18. M. Parrinello and A. Rahman, Polymorphic transitions in single crystals: A new molecular dynamics method, J. Appl. Phys. 52 (1981), pp. 7182-7190.
19. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation, J. Chem. Theory Comput. 4 (2008), pp. 435-447.
20. D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. Mark, and H. Berendsen, GROMACS: Fast, flexible, and free, J. Comput. Chem. 26 (2005), pp. 1701-1718.
21. E. Lindahl, B. Hess, and D. van der Spoel, GROMACS 3.0: A package for molecular simulation and trajectory analysis, J. Mol. Model. 7 (2001), pp. 306-317.
22. H. Berendsen, D. Van der Spoel, and R. Van Drunen, GROMACS: A message-passing parallel molecular dynamics implementation, Comput. Phys. Commun. 91 (1995), pp. 43-56.