3. Applications#

PERFORMING APPLICATIONS

In the third stage, following trajectory extraction, the truncated trajectory file simbox.try.xyz is generated. The MACRO (under development) and MICRO modules can be used for the treatment of biomolecules or for microsolvation analysis, respectively.

PERFORMING THE MICROSOLVATION TREATMENT

In the first step of the microsolvation treatment, the module selects N low-energy clusters, each composed of M solvent molecules. The value of M may be: (1) determined from a prior radial distribution function (RDF) analysis using the DATAS module; (2) defined based on the solute-to-solvent ratio at a user-specified concentration; or (3) calculated automatically, using a cutoff distance corresponding to the diameter of a solvation sphere. The extraction is performed using the following command structure:

solvate ⟨simbox.trj.xyz⟩ -micro [⟨-options⟩]

After this extraction, the selected clusters are stored in the file solute.trj.xyz. In the second step, this file serves as input to optimize the hydrogen bonds within the microsolvation clusters. Subsequently, all microsolvation clusters can be optimized (with constraints, at the xTB level). Finally, the desired properties can be calculated based on user-specified configurations. This procedure is carried out using the following command structure:

solvate ⟨solute.trj.xyz⟩ -micro [⟨-options⟩]

STAGE STRUCTURE