Methods for molecular dynamics

Leforestier C et ak 1991 Time-dependent quantum mechanical methods for molecular dynamics J. Comput. Phys. 94 59-80... 

The ultimate approach to simulate non-adiabatic effects is tln-ough the use of a fiill Scln-ddinger wavefunction for both the nuclei and the electrons, using the adiabatic-diabatic transfomiation methods discussed above. The whole machinery of approaches to solving the Scln-ddinger wavefiinction for adiabatic problems can be used, except that the size of the wavefiinction is now essentially doubled (for problems involving two-electronic states, to account for both states). The first application of these methods for molecular dynamical problems was for the charge-transfer system... 

Okunbor, D.I., Skeel, R.D. Canonical numerical methods for molecular dynamics simulations. J. Comput. Chem. 15 (1994) 72-79. 

B.J. Leimkuhler, S. Reich, and R. D. Skeel. Integration methods for molecular dynamics. In Mathematical approaches to biomolecular structure and dynamics, Seiten 161-185, New York, 1996. Springer. 

R. Elber. Novel methods for molecular dynamics simulations. Curr. Opin. Struc. Biol., 6 232-235, 1996. 

D. Janezic and B. Orel. Implicit Runge-Kutta method for molecular dynamics integration. J. Chem. Info. Comp. Sd., 33 252-257, 1993. 

Janezic, D., Orel, B. Implicit Runge-Kutta Method for Molecular Dynamics Integration. J. Chem. Inf. Comput. Sci. 33 (1993) 252-257 Janezic, D., Orel, B. Improvement of Methods for Molecular Dynamics Integration. Int. J. Quant. Chem. 51 (1994) 407-415... 

Janezic, D., Merzel, F. An Efficient Split Integration Symplectic Method for Molecular Dynamics Simulations of Complex Systems. In Proceedings of the... 

Leimkuhler, B. J., Reich, S., Skeel, R. D. Integration Methods for Molecular Dynamics. In IMA Volumes in Mathematics and its Applications. Eds. Mesirov, J., Schulten, K., Springer-Verlag, Berlin 82 (1995)... 

Garcia-Vela, A., Gerber, R. B. Hybrid quantum-semiclassical wave packet method for molecular dynamics Application to photolysis of Ar...HCl. J. Chem. Phys. 98 (1993) 427-43... 

Plimpton, S., Hendrickson, B. A New Parallel Method for Molecular Dynamics Simulation of Macromolecular Systems. 1994. Technical Report SAND94-1862. Sandia National Laboratories. 

PLS (partial least-squares) algorithm used for 3D QSAR calculations PM3 (parameterization method three) a semiempirical method PMF (potential of mean force) a solvation method for molecular dynamics calculations... 

I. G. Tironi, R. Sperb, P. E. Smith, W. F. van Gunsteren. A generalized reaction field method for molecular dynamics simulations. J Chem Phys 702 5451, 1995. 

Beck DAC, Daggett V. Methods for molecular dynamics simulations of protein folding/unfolding in solution. Methods 2004 34 112-20. 

D.F. Coker and L. Xiao. Methods for molecular-dynamics with nonadiabatic transitions. J. Chem. Phys., 102 496-510, 1995. 

A. R. C. Raine, D. Fincham, and W. Smith, Comput. Phys. Commun., 55, 13 (1989). Systolic Loop Methods for Molecular Dynamics Simulation Using Multiple Transputers. 

A. Raine, Systolic Loop Methods for Molecular Dynamics Simulation, Generalised for Macromolecules, Mol. Simul., 7 (1991), 59-69. 

R. Kosloff, R. (1988) Tiino-dcpciidciit qiiaiitiiin-mcchanical methods for molecular dynamics, J. Phys. Chern. 92, 2087-2100. 

In this chapter we have presented a multi-scale method for molecular dynamics simulations of shock compression and characterized its behaviour. This method attempts to constrain the molecular dynamics system to the sequence of thermodynamic states that occur in a shock wave. While we have presented one particular approach, it is certainly not unique and there are likely a variety of related approaches to multi-scale simulations that have a variety of differing practical properties. These methods open the door to simulations of shock propagation on the longest timescales accessible by molecular d5nnamics and the use of accurate but computationally costly material descriptions like density fimctional theory. It is our belief that this method promises to be a valuable tool for elucidation of new science in shocked condensed matter. 

B. Hartke, R. Kosloff, and S. Ruhman, Large amplitude ground state vibrational coherence induced by impulsive absorption in Csl. A computer simulation. Chem. Phys. Lett. 158 223 (1986). R. Kosloff, Time-dependent quantum-mechanical methods for molecular dynamics, J. Phys. Chem. 92 2087 (1988). 

Swindoll R D and J M Haile 1984. A Mul tiple Time-step Method for Molecular Dynamics Simulations of Fluids of Chain Molecules. Journal of Compututational Physics 53.289-298 Swope W C, H C Anderson, P H Berens and K R Wilson 1982. A Computer Simulation Method for the Calculation of EquBibri-um Constants for the Formation of Physical Clusters of Molecules Application to Small Water Clusters Journal of Chemical Physics 76.637-649 Tobias D J and C L Brooks III 1988 Molecular Dynamics with Internal Coordinate Constraints. Journal of Chemical Physics 89-5115-5126... 

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