Multi-overlap molecular dynamics methods for biomolecular systems

We propose a molecular dynamics method for the multi-overlap algorithm. By utilizing a non-Boltzmann weight factor, this method realizes a random walk in the overlap space at a constant temperature and explores widely in the configurational space, where the overlap of a configuration with respect to a reference state is a measure for structural similarity. We can obtain detailed information about the free-energy landscape and the transition states among any specific reference conformations at that temperature. We also introduce a multi-dimensional extension of the multi-overlap algorithm. Appling this multi-dimensional method to a penta peptide, Met-enkephalin, we demonstrate its effectiveness.

[1]  A Mitsutake,et al.  Generalized-ensemble algorithms for molecular simulations of biopolymers. , 2000, Biopolymers.

[2]  Robert H. Swendsen,et al.  Erratum: ``New Monte Carlo technique for studying phase transitions'' [Phys. Rev. Lett. 61, 2635 (1988)] , 1989 .

[3]  H. Takayama,et al.  APPLICATION OF AN EXTENDED ENSEMBLE METHOD TO SPIN GLASSES , 1996 .

[4]  R A Sayle,et al.  RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.

[5]  Y. Sugita,et al.  Replica-exchange molecular dynamics method for protein folding , 1999 .

[6]  Multioverlap simulations for transitions between reference configurations. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[7]  B. Berg,et al.  Multicanonical algorithms for first order phase transitions , 1991 .

[8]  Y. Okamoto,et al.  Thermodynamics of Helix-Coil Transitions Studied by Multicanonical Algorithms , 1995, chem-ph/9505006.

[9]  Frank Eisenmenger,et al.  Variation of the Energy Landscape of a Small Peptide under a Change from the ECEPP/2 Force Field to ECEPP/3 , 1997, physics/9710020.

[10]  Rupert G. Miller.  The jackknife-a review , 1974 .

[11]  A. Kidera,et al.  Multicanonical Ensemble Generated by Molecular Dynamics Simulation for Enhanced Conformational Sampling of Peptides , 1997 .

[12]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[13]  Y. Okamoto,et al.  Molecular dynamics, Langevin, and hybrid Monte Carlo simulations in multicanonical ensemble , 1996, physics/9710018.

[14]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[15]  H. Scheraga,et al.  Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids , 1975 .

[16]  U H Hansmann,et al.  Temperature dependence of distributions of conformations of a small peptide. , 1998, Journal of molecular graphics & modelling.

[17]  D. Landau,et al.  Efficient, multiple-range random walk algorithm to calculate the density of states. , 2000, Physical review letters.

[18]  Alan M. Ferrenberg,et al.  New Monte Carlo technique for studying phase transitions. , 1988, Physical review letters.

[19]  Yuko Okamoto,et al.  Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system , 2003 .

[20]  U H Hansmann,et al.  Characteristic temperatures of folding of a small peptide. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Berg,et al.  Multicanonical ensemble: A new approach to simulate first-order phase transitions. , 1992, Physical review letters.

[22]  K. Hukushima,et al.  Exchange Monte Carlo Method and Application to Spin Glass Simulations , 1995, cond-mat/9512035.

[23]  H. Scheraga,et al.  Energy parameters in polypeptides. 9. Updating of geometrical parameters, nonbonded interactions, and hydrogen bond interactions for the naturally occurring amino acids , 1983 .

[24]  Berg,et al.  New approach to spin-glass simulations. , 1992, Physical review letters.

[25]  Yuji Sugita,et al.  Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape , 2000, cond-mat/0009119.

[26]  H. Scheraga,et al.  Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H...O = C hydrogen bonds from packing configurations , 1984 .

[27]  Y. Sugita,et al.  Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test , 2003 .