Molecular dynamic procedures

Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data A lac Repressor Headpiece Structure Based on Information on /-Coupling and from Presence and Absence of NOEs. 

We conclude this section by giving a topical example of the utility of conditional averages in considering molecularly complex systems (Ashbaugh et al, 2004). We considered the RPLC system discussed above (p. 5), but without methanol n-Ci8 alkyl chains, tethered to a planar support, with water as the mobile phase. The backside of the liquid water phase contacts a dilute water vapor truncated by a repulsive wall see Fig. 1.2, p. 7. Thus, it is appropriate to characterize the system as consistent with aqueous liquid-vapor coexistence at low pressure. A standard CHARMM force-field model (MacKerell Jr. et al, 1998) is used, as are standard molecular dynamics procedures - including periodic boimdary conditions - to acquire the data considered here. Our interest is in the interface between the stationary alkyl and the mobile liquid water phases at 300 K. 

In summary, this method solves the Schrodinger equation at several intervals of time for the largest possible sample that can be solved with present computational resources. It also creates a force field to compute forces with a classical molecular dynamics procedure in a system containing the largest number of particles that is practical to be used with MD methods. When the time intervals of the ab initio calculations coincide with the time intervals of the molecular dynamics, and when the electron density distribution is used to compute the forces instead of the force field, this method is equivalent to the well known Car-Parrinello method. Evidently, this latter method is limited to a... 

The same applies, in different form though, to a molecular dynamics procedure. The random elements here are the starting point and the initial velocities of the atoms. More or less arbitrarily chosen is the size of the time steps At. 

J. De Vlieg, R. Boelens, R. M. Scheek, R. Kaptein, and W. F. van Gunsteren, hr. J. Chem., 27, 181 (1986). Restrained Molecular Dynamics Procedure for Protein Tertiary Structure Determination from NMR Data A lac Repressor Headpiece Structure Based on Information on J-Coupling and from Presence and Absence of NOE s. 

A non-equilibrium molecular dynamics procedure is used along with an established fixed charge force field. It is foimd that the simulations quantitatively capture the temperature dependence of the viscosity as well as the drop in viscosity that occurs with increasing water content. Using mixture viscosity models, the authors showed that the relative drop in viscosity with water content is actually less than the predicted values for an ideal system. This means that dissolved water is actually less effective at lowering the viscosity of these mixtures when compared to a solute obeying ideal mixing behaviour. 

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