Replica-permutation method to enhance sampling efficiency

References

• Mitsutake A, Sugita Y, Okamoto Y. Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers. 2001;60:96–123.
   PubMed Web of Science ®Google Scholar
• Itoh SG, Okumura H, Okamoto Y. Generalized-ensemble algorithms for molecular dynamics simulations. Mol Simul. 2007;33:47–56.
   Web of Science ®Google Scholar
• Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. Equation of state calculations by fast computing machines. J Chem Phys. 1953;21:1087–1092.
   Web of Science ®Google Scholar
• Nosé S. A molecular-dynamics method for simulations in the canonical ensemble. Mol Phys. 1984;52:255–268.
   Web of Science ®Google Scholar
• Nosé S. A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys. 1984;81:511–519.
   Web of Science ®Google Scholar
• Hoover WG. Canonical dynamics: equilibrium phase-space distributions. Phys Rev A. 1985;31:1695–1697.
   PubMed Web of Science ®Google Scholar
• Okumura H, Itoh SG, Okamoto Y. Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles. J Chem Phys. 2007;126:084103.
   Web of Science ®Google Scholar
• Hukushima K, Nemoto K. Exchange Monte Carlo method and application to spin glass simulations. J Phys Soc Jpn. 1996;65:1604–1608.
   Google Scholar
• Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett. 1999;314:141–151.
   Web of Science ®Google Scholar
• Hansmann UHE, Okamoto Y, Eisenmenger F. Molecular dynamics, Langevin and hybrid Monte Carlo simulations in a multicanonical ensemble. Chem Phys Lett. 1996;259:321–330.
   Web of Science ®Google Scholar
• Nakajima N, Nakamura H, Kidera A. Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides. J Phys Chem B. 1997;101:817–824.
   Web of Science ®Google Scholar
• Berg BA, Neuhaus T. Multicanonical algorithms for first order phase-transitions. Phys Lett B. 1991;267:249–253.
   Web of Science ®Google Scholar
• Berg BA, Neuhaus T. Multicanonical ensemble: a new approach to simulate first-order phase transitions. Phys Rev Lett. 1992;68:9–12.
   PubMed Web of Science ®Google Scholar
• Okumura H, Okamoto Y. Monte Carlo simulations in multibaric-multithermal ensemble. Chem Phys Lett. 2004;383:391–396.
   Web of Science ®Google Scholar
• Okumura H, Okamoto Y. Monte Carlo simulations in generalized isobaric-isothermal ensembles. Phys Rev E. 2004;70:026702.
   Web of Science ®Google Scholar
• Okumura H, Okamoto Y. Liquid–gas phase transitions studied by multibaric-multithermal Monte Carlo simulations. J Phys Soc Jpn. 2004;73:3304–3311.
   Google Scholar
• Okumura H, Okamoto Y. Molecular dynamics simulations in the multibaric-multithermal ensemble. Chem Phys Lett. 2004;391:248–253.
   Web of Science ®Google Scholar
• Okumura H, Okamoto Y. Multibaric-multithermal ensemble molecular dynamics simulations. J Comput Chem. 2006;27:379–395.
   PubMed Web of Science ®Google Scholar
• Berg BA, Noguchi H, Okamoto Y. Multioverlap simulations for transitions between reference configurations. Phys Rev E. 2003;68:036126.
   Web of Science ®Google Scholar
• Itoh SG, Okamoto Y. A new generalized-ensemble algorithm: multicanonical-multioverlap algorithm. Mol Simul. 2007;33:83–89  Symposium on Progress and Future Prospects in Molecular Dynamics Simulation, Keio University, Yokohama, Japan, Jun 06–08, 2006.
   Web of Science ®Google Scholar
• Okumura H. Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations. J Chem Phys. 2008;129:124116.
   PubMed Web of Science ®Google Scholar
• Okumura H. Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water solvent. Phys Chem Chem Phys. 2011;13:114–126.
   PubMed Web of Science ®Google Scholar
• Okumura H. Temperature and pressure denaturation of chignolin: folding and unfolding simulation by multibaric-multithermal molecular dynamics method. Proteins. 2012;80:2397–2416.
   PubMed Web of Science ®Google Scholar
• Suwa H, Todo S. Markov chain Monte Carlo method without detailed balance. Phys Rev Lett. 2010;105:120603.
   PubMed Web of Science ®Google Scholar
• Itoh SG, Okumura H. Replica-permutation method with the Suwa–Todo algorithm beyond the replica-exchange method. J Chem Theory Comput. 2013;9:570–581.
   PubMed Web of Science ®Google Scholar
• Itoh SG, Okumura H. Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β (29–42) peptides. J Comput Chem. 2013;34:2493–2497.
   PubMed Web of Science ®Google Scholar
• Itoh SG, Okamoto Y. Multi-overlap molecular dynamics methods for biomolecular systems. Chem Phys Lett. 2004;400:308–313.
   Web of Science ®Google Scholar
• Itoh SG, Okamoto Y. Theoretical studies of transition states by the multioverlap molecular dynamics methods. J Chem Phys. 2006;124:104103.
   PubMed Web of Science ®Google Scholar
• Itoh SG, Okamoto Y. Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm. Phys Rev E. 2007;76:026705.
   Web of Science ®Google Scholar
• Shoemaker KR, Kim PS, Brems DN, Marqusee S, York EJ, Chaiken IM, Stewart JM, Baldwin RL. Nature of the charged-group effect on the stability of the C-peptide helix. Proc Natl Acad Sci USA. 1985;82:2349–2353.
   PubMed Web of Science ®Google Scholar
• Shoemaker KR, Kim PS, York EJ, Stewart JM, Baldwin RL. Tests of the helix dipole model for stabilization of α-helices. Nature. 1987;326:563–567.
   PubMed Web of Science ®Google Scholar
• Osterhout JJ, Baldwin RL, York EJ, Stewart JM, Dyson HJ, Wright PE. Proton NMR studies of the solution conformations of an analog of the C-peptide of ribonuclease-A. Biochemistry. 1989;28:7059–7064.
   PubMed Web of Science ®Google Scholar
• Fairman R, Shoemaker KR, York EJ, Stewart JM, Baldwin RL. The Glu 2− …ARG 10+ side-chain interaction in the C-peptide helix of ribonuclease-A. Biophys Chem. 1990;37:107–119.
   PubMed Web of Science ®Google Scholar
• Lim D, Moye-Sherman D, Ham I, Jim S, Scholtz JM, Burgess K. 2,3-Methanoamino acid analogs of Arg stabilize secondary structures of a 13 amino acid peptide in aqueous solution. Chem Commun. 1998 :2375–2376.
   Web of Science ®Google Scholar
• Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins. 2006;65:712–725.
   PubMed Web of Science ®Google Scholar
• Sugita Y, Kitao A, Okamoto Y. Multidimensional replica-exchange method for free-energy calculations. J Chem Phys. 2000;113:6042–6051.
   Web of Science ®Google Scholar
• Fukunishi H, Watanabe O, Takada S. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction. J Chem Phys. 2002;116:9058–9067.
   Web of Science ®Google Scholar
• Itoh SG, Okumura H, Okamoto Y. Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules. J Chem Phys. 2010;132:134105.
   PubMed Web of Science ®Google Scholar
• Itoh SG, Damjanović A, Brooks BR. pH replica-exchange method based on discrete protonation states. Proteins. 2011;79:3420–3436.
   PubMed Web of Science ®Google Scholar
• Itoh SG, Okumura H. Coulomb replica-exchange method: handling electrostatic attractive and repulsive forces for biomolecules. J Comput Chem. 2013;34:622–639.
   PubMed Web of Science ®Google Scholar
• Okumura H, Itoh G. Transformation of a design peptide between the α-helix and β-hairpin structures using a helix-strand replica-exchange molecular dynamics simulation. Phys Chem Chem Phys. 2013;15:13852–13861.
   PubMed Web of Science ®Google Scholar