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.

Reference functions

coordination_number(trajectory::Trajectory, options::Options)

Computes the coordination numbers for each solute molecule in the trajectory, given the Trajectory. This is an auxiliary function of the ComplexMixtures package, which is used to compute coordination numbers when the normalization of the distribution is not possible or needed.

The output is a Result structure, which contains the data as the result of a call to mddf, except that all counters which require normalization of the distribution will be zero. In summary, this result data structure can be used to compute the coordination numbers, but not the MDDF, RDF, or KB integrals.


julia> trajectory = Trajectory("./trajectory.dcd",solute,solvent);

julia> results = mddf(trajectory);

julia> coordination_numbers = coordination_number(trajectory);
mddf(trajectory::Trajectory, options::Options; frame_weights = Float64[], coordination_number_only = false)

Function that computes the minimum-distance distribution function, atomic contributions, and KB integrals, given the Trajectory structure of the simulation and, optionally, parameters given as a second argument of the Options type. This is the main function of the ComplexMixtures package.


julia> trajectory = Trajectory("./trajectory.dcd",solute,solvent);

julia> results = mddf(trajectory);

or, to set some custom optional parameter,

julia> options = Options(lastframe=1000);

julia> results = mddf(trajectory,options);