Software: Proteins - Dynamics

Molecular dynamics is a very important tool frequently used in computational biology in order to understand various chemical, kinetic and thermodynamical properties of proteins and polypeptides. 

There are many molecular dynamics software packages available via the Internet, however the package we present here, MOIL, is a special one. It includes many features one cannot find elsewhere, such as:

a) Locally Enhanced Sampling (LES)
b) Landau-Zerner model based approach to instantaneous dissociation and recombination of ligands
c) Stochastic Path (STO) for long time dynamics and other functional approaches to reaction path calculations

One of the main difficulties in MD concerns time scales of various biologically (or chemically) important processes, given the limitation of numerical integrators - the time step used in the standard Verlet algorithm cannot be much larger than just a femtosecond because there are usually fast motions in the system (e.g. vibrations of bonds involving light atoms, for which the time scale is of the order of 10 fs). Thus folding of proteins for instance, which can take seconds, cannot be approached using standard MD. If you want to perform simulations with a much larger time step - use MOIL and STO.