Force Fields, Models and Solvation Approaches

The individual components of a force field reflect established physical principles, such as representing bond lengths and angles as harmonic oscillators, and using Lennard-Jones 12-6 and Coulomb-type functions for the van der Waals and electrostatic nonbonding interactions, respectively. FIow-ever, the force fields are not independent of the protein models used. Each force field has associated with it atomic and molecular definitions and parameters, definitions that will differ between united atom and all-atom representations, for example. Similarly, water models are parameterized for use with certain force fields and are not necessarily interchangeable.  

Force fields are empirically based functions that use experimentally derived parameters for the bond lengths, angles, and force constants. Parameters are typically obtained from small organic molecules or, where experimental data are undetermined, can be calculated using ab initio methods.Ffence, force fields have their limitations, and there have been many force field comparisons performed to assess their accuracy and abilities.Arguably, a stronger assessment of a force field is whether it is able to adequately reproduce experimental observables. It is important to note that many of the force 

TIP5P SPC models, SPC and SPC/E rigid Stillinger and Rahman model, ST2 and the flexible three-centered water model, F3C.  

A simplification that one can use instead of treating the solvent explicitly is to incorporate the solvent contribution by modeling it as a continuous dielectric medium. Such implicit solvation methods are widely used to reduce the computational expense of a simulation. A popular choice is the generalized Born method a review of this method and case studies of its application are contained in Bashford et al.  

Another consideration when using PBC is that calculation of all pairwise nonbonding interactions in such an infinite system would be computationally 

---