Molecular dynamics simulations predictive methods

All previously discussed methods are primarily based on phenomenological considerations, in contrast to chapter six (K. Binder et al.), which starts from statistical thermodynamics. This section reviews the state of the art in fields of Mraite-Carlo and Molecular Dynamics simulations. These methods are powerful tools for the prediction of macroscopic properties of matter from suitable models for effective interactions between atoms and molecules. The final chapter (G. Sadowski) makes use of the results obtained with simulation tools for the establishment of molecular-based equations of state for engineering applications. This approach enables the description and in some cases even the prediction of the phase behavior as a function of pressure, temperature, molecular weight distribution and for copolymers also as a function of chemical composition. 

There are many variants of the predictor-corrector theme of these, we will only mention the algorithm used by Rahman in the first molecular dynamics simulations with continuous potentials [Rahman 1964]. In this method, the first step is to predict new positions as follows ... 

The strong point of molecular dynamic simulations is that, for the particular model, the results are (nearly) exact. In particular, the simulations take all necessary excluded-volume correlations into account. However, still it is not advisable to have blind confidence in the predictions of MD. The simulations typically treat the system classically, many parameters that together define the force field are subject to fine-tuning, and one always should be cautious about the statistical certainty. In passing, we will touch upon some more limitations when we discuss more details of MD simulation of lipid systems. We will not go into all the details here, because the use of MD simulation to study the lipid bilayer has recently been reviewed by other authors already [31,32]. Our idea is to present sufficient information to allow a critical evaluation of the method, and to set the stage for comparison with alternative approaches. 

At present we are far from an understanding of the protein folding process. Even numerical methods as e.g. molecular dynamics simulations do not lead to realistic predictions. Experiments on the folding process have been performed initially on the millisecond time-scale. It was only recently that new techniques - temperature jump or triplet-triplet quenching experiments - allowed a first access to the nanosecond time domain [2-4]. However, the elementary reactions in protein folding occur on the femto- to picosecond time-scale (femtobiology). In order to allow experiments in this temporal range we developed a new... 

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