Molecular dynamics constrained

The steepest descent (4.48) requires calculation of dA/d . Laio and Parrinello chose to estimate this term by performing short constrained molecular dynamics simulations and computing the potential of mean constraint force (see Carter et al. [45]). 

Sprik, M. Ciccotti, G., Free energy from constrained molecular dynamics, J. Chem. Phys. 1998,109, 7737-7744... 

Refine the structure by use of constrained molecular dynamics and molecular mechanics routines. 

D. C. Fry, V. S. Madison, D. R. Bolin, D. N. Greeley, V. Toome, and B. B. Wegrzynski, Biochemistry, 28, 2399 (1989). Solution Structure of an Analogue of Vasoactive Intestinal Peptide as Determined by Two-Dimensional NMR and Circular Dichroism Spectroscopies and Constrained Molecular Dynamics. 

E. Guardia, R. Rey and J.A. Padro, Potential of mean force by constrained molecular dynamics a sodium chloride ion pair in water, Chem. Phys., 155 (1991) 187-195. 

G. Ciccotti, M. Ferrario, J. T. Hynes, and R. Kapral, Constrained molecular dynamics and the mean potential for an ion pair in a polar solvent, Chem. Phys. 129 (1989) 241. 

We have studied the intracage oxidation of nitrite sodalite to nitrate sodalite by using the Constrained Molecular Dynamics (Blue Moon Ensemble) method [4, 5] together... 

Fig. 8 Model system for a 20,000-step constrained molecular dynamics...

R. Edberg, D. J. Evans, and G. P. Morriss, /. Chem, Phys., 84, 6933 (1986). Constrained Molecular Dynamics Simulations of Liquid Alkanes with a New Algorithm. 

An alternative, simpler, and probably more robust, procedure is simply to fix the value of A(q) by constraining q to its mechanical equilibrium value [189] in which case no fast averaging whatsoever needs to be performed. This approach relies on the use of the SHAKE method of constrained molecular dynamics (see the following section). 

Edberg, R., Evans, D., Moriiss, G. Constrained molecular dynamics simulations of liquid alkanes with a new algorithm. J. Chem. Phys. 84, 6933-6939 (1986). doi 10.1063/1.450613... 

Guardia, E. Rey, R. Padro, J. A. (1991) Potential of Mean Force by Constrained Molecular Dynamics A Sodium Chloride Ion-pair in Water, Chemical Physics 155, 187-195... 

Ciccotti, G. Ferrario, M. Hynes, J. T. Kapral, R. (1989) Constrained Molecular Dynamics and the Mean Potential for an Ion Pair in a Polar Solvent, Chemical Physics 129, 241-251... 

Vaidehi N, Jain A, Goddard WA (1996) Constant temperature constrained molecular dynamics The Newton-Euler inverse mass operator method. J Phys Chem 100(25) 10508-10517... 

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