Adaptive conformational sampling based on replicas
Computer simulations of biomolecules such as molecular dynamics simulations are limited by the time scale of conformational rearrangements. Several sampling techniques are available to search the multi-minima free energy landscape but most efficient, time-dependent methods do generally not produce a canonical ensemble. A sampling algorithm based on a self-regulating ladder of searching copies in the dihedral subspace is developped in this paper. The learning process using short- and long-term memory functions allows an efficient search in phase space while combining a deterministic dynamics and stochastic swaps with the searching copies conserves a canonical limit. The sampling efficiency and accuracy are indicated by comparing the ansatz with conventional molecular dynamics and replica exchange simulations.
KeywordsAdaptive sampling Convergence of molecular dynamics Replica exchange Dihedral angles
Mathematics Subject Classification (2000)82B05 82C05
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- Berg BA, Neuhaus T (1991) Multicanonical algorithms for first order phase transitions. Phys Lett B B267: 53–249Google Scholar
- Beveridge DL, Barreiro G, Byun KS, Case DA, Cheatham TE III, Dixit SB, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Seibert E, Sklenar H, Stoll G, Thayer KM, Varnai P, Young MA (2004) Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides: I Research design, Informatics, and results on CpG steps. Biophys J 87: 3799–3813CrossRefGoogle Scholar
- Birkhoff G (1931) Proof of the ergodic theorem. Proc Natl Acad Sci USA 17: 656660Google Scholar
- Case DA, Darden TA, Cheatham TE III, Simmerling CL, Wang J, Duke RE, Luo R, Maerz KM, Wang B, Pearlman DA, Crowley M, Brozell S, Tsui V, Gohlke H, Mongan J, Hornak V, Cui G, Beroza P, Schafmeister C, Caldwell JW, Ross WS, Kollman PA (2004) AMBER 8 University of California, San FranciscoGoogle Scholar
- Curuksu J (2009) Conformational sampling by molecular mechanics and dynamics simulations applied to the flexibility of nucleic acids. Dissertation, Jacobs UniversityGoogle Scholar
- Huber T, Torda AE, Van Gunsteren WF (1994) Local elevation: a method for improving the searching properties of molecular dynamics simulation. J CAMD 8: 695–708Google Scholar
- Leach AR (1996) Molecular modelling. Principles and applications. Addison Wesley, Singapore, pp 356–358Google Scholar
- Marsili S, Barducci A, Chelli R, Procacci P, Schettino V (2006) Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations. J Phys Chem 110: 3–14011Google Scholar
- Mesirov JP, Schulten K, Sumners DW (1996) Mathematical applications to biomolecular structure and dynamics, IMA volumes in mathematics and its applications. Springer, New York pp 218–247Google Scholar
- Wang F, Landau DP (2001) Efficient, multiple-range random walk algorithm to calculate the density of state. Phys Rev Lett 86: 3–2050Google Scholar