Single molecular dynamics simulations

Marrink, S.J., Jahnig, F., Berendsen, H.J.C. Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations. Biophys. J. 71 (1996) 632-647. 

To calculate the properties of a molecule, you need to generate a well-defined structure. A calculation often requires a structure that represents a minimum on a potential energy surface. HyperChem contains several geometry optimizers to do this. You can then calculate single point properties of a molecule or use the optimized structure as a starting point for subsequent calculations, such as molecular dynamics simulations. 

In contrast to the single molecule case, Monte Carlo methods tend to be rather less efficient than molecular dynamics in sampling phase space for a bulk fluid. Consequently, most of the bulk simulations of liquid crystals described in Sect. 5.1 use molecular dynamics simulation methods. 

We now describe a different approach which is simpler than the method of constraints and also very efficient. It does not require running a constrained simulation and can be performed entirely with a single molecular dynamics run. 

Even if we consider a single solvent, e g., water, at a single temperature, say 298K, depends on the solute and in fact on the coordinate of the solute which is under consideration, and we cannot take xF as a constant. Nevertheless, in the absence of a molecular dynamics simulation for the solute motion of interest, XF for polar solvents like water is often approximated by the Debye model. In this model, the dielectric polarization of the solvent relaxes as a single exponential with a relaxation time equal to the rotational (i.e., reorientational) relaxation time of a single molecule, which is called Tp) or the Debye time [32, 347], The Debye time may be associated with the relaxation of the transverse component of the polarization field. However the solvent fluctuations and frictional relaxation occur on a faster scale given by [348,349]... 

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