Molecular dynamics simulation different techniques

Straatsma, T.P, Berendsen, H.J.C. Free energy of ionic hydration Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations. J. Chem. Phys. 89 (1988) 5876-5886. 

The thermodynamic properties that we have considered so far, such as the internal energy, the pressure and the heat capacity are collectively known as the mechanical properties and can be routinely obtained from a Monte Carlo or molecular dynamics simulation. Other thermodynamic properties are difficult to determine accurately without resorting to special techniques. These are the so-called entropic or thermal properties the free energy, the chemical potential and the entropy itself. The difference between the mechanical emd thermal properties is that the mechanical properties are related to the derivative of the partition function whereas the thermal properties are directly related to the partition function itself. To illustrate the difference between these two classes of properties, let us consider the internal energy, U, and the Fielmholtz free energy, A. These are related to the partition function by ... 

Numerous studies have been performed in order to elucidate the structure and the dynamics of confined water using a variety of experimental techniques — NMR, quasi-electron neutron diffraction, IR absorption spectroscopy, or molecular dynamics simulation. Most of these studies use model porous media such as clays, polymer membranes, different types of silica and zeolites. Some of these systems (cf Fig. 2) may be used to study water radiolysis in nanoporous media. 

To address the docking problem, techniques for a more global exploration of the en-ag/ landscape are required. A variety of methods is available, frequently used in the context cf other modeling applications and optimization problems as well. Three major classes may be distinguished Monte Carlo techniques, molecular dynamics simulations, and genetic algorithms. Many different vari-fants exist for all of them and frequently, in... 

Straatsma, T. P. and H. J. C. Berendsen (1988). Free Energy of Ionic Hydration Analysis of a Thermodynamic Technique to Evaluate Free Energy Differences by Molecular Dynamics Simulations. L Chem. Phvs. 89(9) 5876. 

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