Molecular dynamics results analysis

This work has indicated that VTST may be a useful method for calculating solution rate constants and thereby helping to understand solution reaction dynamics through analysis of the solution transition state surface. However, for this to occur, a simple prescription must be developed for applying VTST to solution systems where full molecular dynamics can be performed, much in the way that Grote-Hynes theory has been used to understand a wide variety of molecular dynamics results. Work by Hahn and Pollak o is proceeding in this direction through the application of VTST to the Cl -I- CHjCI Sn2 reaction in aqueous solution discussed elsewhere in this review.(A closely related study is the VTST work by Tucker and Truhlar on the mono- and dihydrated versions of this S 2 reaction.)... 

As a challenging example of vibrational analysis via a time-dependent approach, we choose the hexa-aquo complex of the Zn(II) ion in aqueous solution, which has been extensively studied both theoretically [99-102] and experimentally [101]. Several methodologies aimed to analyze EXAFS spectra include molecular dynamics results. 

We have emphasized the comparison between molecular dynamics results and continuum theory analysis. This is felt to be essential for demonstrating that the effects described by a macroscopic theory can be simulated in terms of particle dynamics. 

G. Ravishanker (ed.), Molecular Dynamics Toolchest Analysis and Graphical Display of Computer Simulation Results on Proteins and Nucleic Acids , Wesleyan University, Middle-town, CT, 1991. 

An important issue, the significance of which is sometime underestimated, is the analysis of the resulting molecular dynamics trajectories. Clearly, the value of any computer simulation lies in the quality of the information extracted from it. In fact, it is good practice to plan the analysis procedure before starting the simulation, as the goals of the analysis will often detennine the character of the simulation to be performed. 

One of the main attractions of normal mode analysis is that the results are easily visualized. One can sort the modes in tenns of their contributions to the total MSF and concentrate on only those with the largest contributions. Each individual mode can be visualized as a collective motion that is certainly easier to interpret than the welter of information generated by a molecular dynamics trajectory. Figure 4 shows the first two normal modes of human lysozyme analyzed for their dynamic domains and hinge axes, showing how clean the results can sometimes be. However, recent analytical tools for molecular dynamics trajectories, such as the principal component analysis or essential dynamics method [25,62-64], promise also to provide equally clean, and perhaps more realistic, visualizations. That said, molecular dynamics is also limited in that many of the functional motions in biological molecules occur in time scales well beyond what is currently possible to simulate. 

The MYD analysis assumes that the atoms do not move as a result of the interaetion potential. The eonsequenees of this assumption have recently been examined by Quesnel and coworkers [50-55], who used molecular dynamic modeling techniques to simulate the adhesion and release of 2-dimensional particles from 2-D substrates. Specifically, both the Quesnel and MYD models assume that the atoms in the different materials interact via a Lennard-Jones potential

[Pg.153]

Fig. 7 gives an example of such a comparison between a number of different polymer simulations and an experiment. The data contain a variety of Monte Carlo simulations employing different models, molecular dynamics simulations, as well as experimental results for polyethylene. Within the error bars this universal analysis of the diffusion constant is independent of the chemical species, be they simple computer models or real chemical materials. Thus, on this level, the simplified models are the most suitable models for investigating polymer materials. (For polymers with side branches or more complicated monomers, the situation is not that clear cut.) It also shows that the so-called entanglement length or entanglement molecular mass Mg is the universal scaling variable which allows one to compare different polymeric melts in order to interpret their viscoelastic behavior. 

In the next section we describe the basic models that have been used in simulations so far and summarize the Monte Carlo and molecular dynamics techniques that are used. Some principal results from the scaling analysis of EP are given in Sec. 3, and in Sec. 4 we focus on simulational results concerning various aspects of static properties the MWD of EP, the conformational properties of the chain molecules, and their behavior in constrained geometries. The fifth section concentrates on the specific properties of relaxation towards equilibrium in GM and LP as well as on the first numerical simulations of transport properties in such systems. The final section then concludes with summary and outlook on open problems. 

---