Molecular dynamics solutions

Hammes-Schiffer, S., Tully, J.C. Proton transfer in solution Molecular dynamics with quantum transitions. J. Chem. Phys. 101 (1994) 4657 667. 

Although one cannot simulate an electrolyte solution, molecular-dynamics studies of an ensemble of water with one or two ions have been performed. The long-range nature of the Coulomb force causes considerable technical difficulties in addition, the interaction potentials are somewhat uncertain. So the results have to be considered with caution. Nevertheless, they seem reasonable, and fit in well with our knowledge of the interface. Figure 17.9 shows the results of a simulation of an ensemble of water molecules with one Li+ and one I"" ion in the presence of a fairly large field between the two metal plates [14]. In... 

Once the boundary conditions have been implemented, the calculation of solution molecular dynamics proceeds in essentially the same manner as do vacuum calculations. While the total energy and volume in a microcanonical ensemble calculation remain constant, the temperature and pressure need not remain fixed. A variant of the periodic boundary condition calculation method keeps the system pressure constant by adjusting the box length of the primary box at each step by the amount necessary to keep the pressure calculated from the system second virial at a fixed value (46). Such a procedure may be necessary in simulations of processes which involve large volume changes or fluctuations. Techniques are also available, by coupling the system to a Brownian heat bath, for performing simulations directly in the canonical, or constant T,N, and V, ensemble (2,46). 

S. E. Debolt and P. A. Kollman. Investigation of structure, dynamics, and solvation in 1-octanol and its water-saturated solution - molecular-dynamics and free-energy perturbation studies. J. Am. Chem. Soc., 117(19) 5316—5340, 1995. 

Troxler, L., Harrowfield, J. M., Wipff, G. (1998), Do Picrate Anions "Attract Each Other" in Solution Molecular Dynamics Simulations in Water and in Acetonitrile Solutions,/. Phys. Chem. A 102, 6821-6830. 

It is increasingly being recognized that the solution molecular dynamics of drugs may have an important role in modulating biological ac-... 

Which of the two computer simulation methods is more efficient in accurately simulating (i) static and (ii) dynamic properties of a single polymer chain in dilute solution molecular dynamics with explicit solvent or Brownian dynamics without explicit solvent ... 

Donnamaria, M.C., Howard, E.I., and Grigera, J.R. Interaction of water with a,a-trehalose in solution — molecular dynamics simulation approach, /. Chem. Soc. Faraday Trans., 90, 2731, 1994. 

Zeolites can contain charge-compensating cations. These cations can be mobile and can be exchanged, usually with an aqueous solution. Molecular dynamics simulations of the cation mobility in anhydrous zeolite A have been performed by Shin et al.2S2 Xhe most complete studies to date of a real zeolite are molecular dynamics simulations of zeolite A containing both sodium cations and water.283-285... 

Alamethicin Helices in a Bilayer and in Solution Molecular Dynamics Simulations. 

Carrillo YJ-M, Dobrynin AV (2011) Polyelectrolytes in salt solutions molecular dynamics simulations. Macromolecules 44 5798-5816. doi 10.1021/ ma2007943... 

Tieleman DP, Sansom MSP, Berendsen HJC (1999) Alamethicin helices in a bilayer and in solution molecular dynamics simulations. Biophys J 76(l) 40-49... 

A Malevanets and R. Kapral, Solute molecular dynamics in a mesoscale solvent,/ Chem. Phys., 112, 7260-7269 (2000). 

Eiao, Q., Carrillo, J.Y., Dobrynin, A.V., Rubinstein, M. Rouse dynamics of polyelectrolyte solutions molecular dynamics study. Macromolecules 40, 7671-7679 (2007)... 

Solution - Molecular-Dynamics with Quantum Transitions. 

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