Optimal allocation of replicas in parallel tempering simulations.
暂无分享,去创建一个
[1] Haruo Abe,et al. Noninteracting local‐structure model of folding and unfolding transition in globular proteins. II. Application to two‐dimensional lattice proteins , 1981, Biopolymers.
[2] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[3] Wang,et al. Replica Monte Carlo simulation of spin glasses. , 1986, Physical review letters.
[4] R. Swendsen,et al. THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .
[5] K. Hukushima,et al. Exchange Monte Carlo Method and Application to Spin Glass Simulations , 1995, cond-mat/9512035.
[6] U. Hansmann. Parallel tempering algorithm for conformational studies of biological molecules , 1997, physics/9710041.
[7] J. Skolnick,et al. An Efficient Monte Carlo Model of Protein Chains. Modeling the Short-Range Correlations between Side Group Centers of Mass , 1998 .
[8] J. Skolnick,et al. Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model , 1998, Proteins.
[9] M. Karplus,et al. Effective energy function for proteins in solution , 1999, Proteins.
[10] Y. Sugita,et al. Replica-exchange molecular dynamics method for protein folding , 1999 .
[11] P Rotkiewicz,et al. A method for the improvement of threading‐based protein models , 1999, Proteins.
[12] Y. Sugita,et al. Multidimensional replica-exchange method for free-energy calculations , 2000, cond-mat/0009120.
[13] Helix‐coil and beta sheet‐coil transitions in a simplified, yet realistic protein model , 2000 .
[14] J. Pablo,et al. Hyperparallel tempering Monte Carlo simulation of polymeric systems , 2000 .
[15] Nancy C. Ekdawi-Sever,et al. Molecular Simulation of Sucrose Solutions near the Glass Transition Temperature , 2001 .
[16] Berend Smit,et al. Understanding Molecular Simulation , 2001 .
[17] D. Landau,et al. Efficient, multiple-range random walk algorithm to calculate the density of states. , 2000, Physical review letters.
[18] David A. Kofke,et al. ARTICLES On the acceptance probability of replica-exchange Monte Carlo trials , 2002 .
[19] Marek Cieplak,et al. Folding and stretching in a Go‐like model of titin , 2001, Proteins.
[20] Juan J. de Pablo,et al. Monte Carlo simulation of proteins through a random walk in energy space , 2002 .
[21] J. Pablo,et al. Multicanonical parallel tempering , 2002, cond-mat/0201179.
[22] K. Sanbonmatsu,et al. Structure of Met‐enkephalin in explicit aqueous solution using replica exchange molecular dynamics , 2002, Proteins.
[23] J. Pablo,et al. Density of states simulations of proteins , 2003 .
[24] J. D. de Pablo,et al. Configurational temperature density of states simulations of proteins. , 2003, Biophysical journal.
[25] F. Escobedo,et al. Expanded ensemble and replica exchange methods for simulation of protein-like systems , 2003 .
[26] Q. Yan,et al. Fast calculation of the density of states of a fluid by Monte Carlo simulations. , 2003, Physical review letters.