Computing the Minimum-Distance Distribution Function

The main function of the ComplexMixtures package actually computes the MDDF between the solute and the solvent chosen.

It is run with the following command:

results = mddf(trajectory)  

The MDDF along with other results, like the corresponding KB integrals, are returned in the results data structure, which is described in the next section.

It is possible to tune several options of the calculation, by setting the Options data structure with user-defined values in advance. The most common parameters to be set by the user are probably dbulk and stride.

dbulk defines the distance from the solute above which the user believes that the reference solute molecule does not significantly anymore the structure of the solvent. The default value is 10 Angstroms, but for large solvent molecules this might not be enough. To increase dbulk, use:

options = Options(dbulk=15.)
results = mddf(trajectory,options)

stride defines if some frames will be skip during the calculation (for speedup). For example, if stride=5, only one in five frames will be considered. Adjust stride with:

options = Options(stride=5)
results = mddf(trajectory,options)

See the Options section for further details and other options to set.