Molecular dynamics accelerated

Voter, A.F., Hyperdynamics Accelerated molecular dynamics of infrequent events, Phys. Rev. Lett. 1997, 78, 3908-3911... 

Hamelberg, D. Mongan, J. McCammon, J.A., Accelerated molecular dynamics a promising and efficient simulation method for biomolecules, 7. Chem. Phys. 2004,120, 11919-11929... 

Accelerated Molecular Dynamics Methods Introduction and Recent Developments... 

Mishin, Y., Suzuki, A., Uberuaga, B.P., Voter, A.F. Stick-slip behavior of grain boundaries studied by accelerated molecular dynamics. Phys. Rev. B 2007, 75, 224101-1-7. 

Becker, K.E., Mignogna, M.H., Fichthorn, K.A. Accelerated molecular dynamics of temperature-programmed desorption. Phys. Rev. Lett. 2009, 102, 046101-1—1. 

Uberuaga, B.P., Montalenti, E, Germann, T.C., Voter, A.F Accelerated molecular dynamics methods. In Handbook of Materials Modeling, Part A Methods (ed. S. Yip), Springer, Dordrecht, The Netherlands, 2005, p. 629. 

Hamelberg D, Mongan J, McCammon JA (2004) Enhanced sampling of conformational transitions in proteins using full atomistic accelerated molecular dynamics simulations. Protein Sci 13 76-76... 

Recent single-molecule experimental studies of proteins provide more detailed views of protein motions, and confirm that a wide variety of timescales is involved in, e.g., catalytic action of enzymes [7,14,15,19,33], Of course, molecular dynamics simulations have been used to probe motions in single proteins for many years, and advances in both theory and computational science have made simulations a powerful approach to building theoretical understanding of protein dynamics [1], The recent introduction of accelerated molecular dynamics methods is helpful in this context [11]. Although detailed dynamical information is sacrificed to the enhanced sampling of conformational space in these methods, which have been shown to access conformational fluctuations that are revealed by nuclear magnetic resonance experiments on the millisecond... 

Yang, J., Wang, Y., Chen, Y. GPU accelerated molecular dynamics simulation of thermal conductivities. J. Comput. Phys. 2007, 221, 799-804. 

Voter A. R, Hyperdynamics Accelerated Molecular Dynamics of Infrequent Events, Phys. Rev. 

We have also developed a second hybrid EF/CG scheme for use when the Hessian is unavailable [82]. A variational approach is used to find the smallest eigenvalue and corresponding eigenvector [127] Voter has recently employed a similar method to accelerate molecular dynamics simulations of rare events in solids [128]. 

Miron, R.A., Fichthom, K.A. Accelerated molecular dynamics with the bond-boost method, J. Chem. Phys. 2003,119,6210. 

Friedrichs, M. S., et al.. Accelerating molecular dynamic simulation on graphics processing units./. Comput Chem., 2009. 30[6), 864-872. 

In addition to providing a microscopic tool for observing the outcomes of physicochemical processes in extraordinary detail, molecular dynamics simulations can, in principle, provide a valuable technique for obtaining thermodynamic variables and rate constants via integration over selected portions of the molecular dynamics trajectory. Several techniques have heen recently employed that allow this kind of analysis, even with the present hmitations regarding length and timescales, such as time-accelerated molecular dynamics [228, 229]. 

---