Multiple molecular dynamics

LSD Caves, JD Evanseck, M Karplus. Locally accessible conformations of proteins Multiple molecular dynamics simulations of crambm. Protein Sci 7 649-666, 1998. 

Caves, L. S., Evanseck, J. D. and Karplus, M. (1998). Locally accessible conformations of proteins multiple molecular dynamics simulations of crambin. Protein Sci, 7, 649-666. 

Worth, G., Nardi, F. and Wade, R. C. (1998). Use of multiple molecular dynamics trajectories to study biomolecules in solution The YTGP peptide. J. Phys. Chem., in press. 

P. Auffinger, S. Louise-May, and E. Westhof, J. Chem. Soc., 117, 6720 (1995). Multiple Molecular Dynamics Simulations of the Anticodon Loop of tRNA in Aqueous Solution with Counterions. 

A = adenine C = cytosine FEP = free energy perturbation G = guanine MMD = multiple molecular dynamics PME = particle mesh Ewald PMF = potential of mean force T = thymine U = uracil. 

Figure 3 Time dependent root mean square (rms) deviation. from the starting crystal structure for the three different sets of multiple molecular dynamics (MMD) trajectories of the tRNA " anticodon hairpin, each using a different method for the evaluation of the electrostatic long-range interactions. The model increases in accuracy from the top graph to the bottom one...

Berne B J 1985 Molecular dynamics and Monte Carlo simulations of rare events Multiple Timescales ed J V Brackbill and B I Cohen (New York Academic Press)... 

Tuckerman M, Berne B J and Martyna G J 1992 Reversible multiple time scale molecular-dynamics J. Chem. Phys. 97 1990-2001... 

Procacci P, March M and Martyna G J 1998 Electrostatic calculations and multiple time scales in molecular dynamics simulation of flexible molecular systems J. Chem. Phys. 108 8799-803... 

In its most fiindamental fonn, quantum molecular dynamics is associated with solving the Sclirodinger equation for molecular motion, whether using a single electronic surface (as in the Bom-Oppenlieimer approximation— section B3.4.2 or with the inclusion of multiple electronic states, which is important when discussing non-adiabatic effects, in which tire electronic state is changed [15,16, YL, 18 and 19]. 

Hammes-Schiffer S and Tully J C 1995 Nonadiabatic transition state theory and multiple potential energy surfaces molecular dynamics of infrequent events J. Chem. Phys. 103 8528... 

Monte Carlo simulations generate a large number of confonnations of tire microscopic model under study that confonn to tire probability distribution dictated by macroscopic constrains imposed on tire systems. For example, a Monte Carlo simulation of a melt at a given temperature T produces an ensemble of confonnations in which confonnation with energy E. occurs witli a probability proportional to exp (- Ej / kT). An advantage of tire Monte Carlo metliod is tliat, by judicious choice of tire elementary moves, one can circumvent tire limitations of molecular dynamics techniques and effect rapid equilibration of multiple chain systems [65]. Flowever, Monte Carlo... 

Tuckerman, M., Berne, B.J., Martyna, G.J. Reversible multiple timescale molecular dynamics. J. Chem. Phys. 97 (1992) 1990-2001. 

Hammes-Schiffer Multiconflgurational molecular dynamics with quantum transitions Multiple proton transfer reactions. J. Chem. Phys. 105 (1996) 2236-2246. 

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. 

W. B. Streett, D. J. Tildesley, and G. Saville. Multiple time step methods in molecular dynamics. Mol. Phys., 35 639-648, 1978. 

Mark E. Tuckerman, Glenn J. Martyna, and Bruce J. Berne. Molecular dynamics algorithm for condensed systems with multiple time scales. J. Chem. Phys., 93(2) 1287-1291, Jul. 1990. 

D. D. Humphreys, R. A. Friesner, and B. J. Berne. Simulated annealing of a protein in a continuum solvent by multiple-time-step molecular dynamics. J. Phys. Chem., 99 10674-10685, 1995. 

M. E. Tuckerman and B. J. Berne. Molecular dynamics in systems with multiple time scales Systems with stiff and soft degrees of freedom and with short and long range forces. J. Comp. Chem., 95 8362-8364, 1992. 

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