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Force fields

The AMBER [51,52], the CHARMM [53,54], the OPLS [55] and the GROMOS force field [56] are the most widely used set of parameters applied to the simulation of biomolecules.

There are studies that perform benchmarks to compare between some of these force fields [57]. The first thing that one must realize is that their set of parameters are different. This is by no means strange because the parameterization process, the atom types and the reference data is different for all of them. So, for example, the atomic partial charges do differ in some magnitude between two force fields. In this sense, we must not give much chemical interpretation to the particular parameters, but they must be seen rather as a set of variables that must adjust to give a global good fitting. This is why all these force fields tend to give similar global results. It means for example, that after a Molecular Dynamics simulation some properties such as the conformation distribution is similar in any force field. It is also true that some specific failures of a force field in certain systems have been reported [54].


next up previous contents
Next: Hybrid methods Up: Molecular Mechanics Previous: Long range interactions   Contents
Xavier Prat Resina 2004-09-09