Molecular Dynamics Systems CHARMM

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. 

There are several MM force fields available, such as OPLS [29], CHARMM [30], AMBER [31], GROMOS [32], MMFF [33], CVFF [34], to mention a few. Several of them have been combined with the QM calculation programs and used in the combined QM/MM molecular dynamics simulations. [12,15,35,36] In our own work we have combined either GAUSSIAN94 [24] or GAMESS [25] with our own simulation software which is the modified version of McMOLDYN [37] package to study solvation phenomena and radical systems [38,39]. 

The CHARMM code, version c25bl, was chosen for integration with the metal potential. CHARMM is a multi-purpose molecular dynamics program [35], which uses empirical potential energy functions to simulate a variety of systems, including proteins, nucleic acids, lipids, sugars and water. The availability of periodic boundary conditions of various lattice types (for example cubic and orthorhombic) makes it possible to treat solids as well as liquids. 

Molecular mechanics minimization and molecular dynamics were chosen to examine the possible conformations for the two acyl enzymes and conclusions were drawn from the time evolution of the two systems. The starting point was a crystal structure of phenylethaneboronic acid bound to alpha-chymotrypsin. QUANTA/CHARMM (Brooks et al, 1983) was employed for the calculations. Ninety-five water molecules from the X-ray structure were included. Distance monitoring and the creation ofH-bonds were the main criteria for differentiating between the two molecules. Both acyl enzymes have their ketone carbonyls H-bonded to Gly-216 NH. Both start with their ester carbonyl in the oxyanion hole (H-bonded to Ser-195 and to Gly-193). The R-acyl enzyme looses both of these hydrogen bonds during the simulation. Attack of water on the R-species should, thus, be less frequently successful. Values for differences in energy were not used because of a small... 

Relative pK calculations are the main method used to determine pK shifts in biomolecular systems. Such calculations have error bars of several pK units for the determination of the pK values for amino acid side chains on a protein [155-157], Because biomolecular systems such as proteins are very large, molecular dynamics simulations use empirical potentials such as AMBER, CHARMM, and OPLS [52], Correspondingly, solvation models are fitted [158] for use with empirical potentials, such as Sharma and Kaminski s fuzzy-border continuum model [159],... 

Previously, the sodium dodecyl sulfate (SDS) surfactant system was also investigated with a 200 ps molecular dynamics computer simulation in the NVT-ensemble (7). In this computer simulation, the parameters of the atomic interaction potential functions were taken from the CHARMM force field. The calculations showed that the SDS micelle remains spherical with a radius of gyration in good agreement with the experimental results. Remarkable motions of the head-groups were observed and the trans to gauche populations are equivalent for the micelle and the analogous hydrocarbon, liquid dodecane. Recently, atomic-level studies of AOT reverse micelles and molecular dynamics simulations of the structure and dynamics of a dode-cylphosphocholine micelle in aqueous solution have been published (8, 9). 

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