Electrolyte Analysis Calculations Panel

Analyze the coordination environment of transference ions in electrolytes from molecular dynamics trajectories. The coordination can be used to analyze the ion transport characteristics of electrolytes.

To open this panel: click the Tasks button and browse to Materials → Classical Mechanics → Trajectory Analysis → Electrolyte Analysis Calculations.

The following licenses are required to use this panel: MS Maestro

  • Using
  • Features
  • Additional Resources

Using the Electrolyte Analysis Calculations Panel

The input for this panel is a trajectory from an MD simulation. You can run MD simulations using the MD Multistage Workflow Panel or the Diffusion Coefficient Panel.

If the system contains multiple cationic molecule types, you can select the one to use as the transference ion. Likewise, you can select the anionic molecule type to be used as the counterion for the analysis. You must also select the coordination elements from the counterion to track. If the system contains additional species such as polymer chains, you can select chain coordination elements as well.

The calculation iterates over each trajectory frame in the selected range and identifies atoms of the selected coordination elements that are within the coordination cutoff distance of each transference ion. Coordination statistics are accumulated across all analyzed frames.

The trajectory frame range determines which portion of the MD simulation is analyzed. Adjusting the start frame allows you to exclude the initial equilibration period, where the system has not yet reached a steady state. The step size option reduces computation time by sampling every Nth frame rather than analyzing every frame.

In addition to the core coordination analysis, you can optionally calculate the radial distribution function (RDF) between the transference ion and all coordination elements, a density isosurface of the transference ion around the counterion, the structure factor S(q), residence times for molecules in the coordination shell, and cluster composition. These options are controlled by checkboxes on the panel.

When the job completes, a new entry group is created in the Project Table with structures extracted from the last frame in the analyzed range. The first entry shows all coordination clusters in the system, with non-cluster atoms hidden. The remaining entries show each transference ion with its coordination sphere, individually. These structures are provided as a visual reference for the coordination environment.

The coordination data, chain coordination, cluster composition, and other results plotted in the viewer are computed across all frames in the selected trajectory range. The Project Table structures show only the last analyzed frame and are independent of the plotted data.

You can plot the results of the calculation using the Electrolyte Analysis Viewer Panel (click the Tasks button and browse to Materials → Classical Mechanics → Trajectory Analysis → Electrolyte Analysis Results). To open this panel from the entry group for the results of a job, and load the results, use the Workflow Action Menu .

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see electrolyte_analysis_driver.py Command Help.

Electrolyte Analysis Calculations Panel Features

Load from Workspace button

Load the trajectory that is associated with the structure in the Workspace.

Trajectory Frames button

Set the range and interval of trajectory frames to use in the analysis. The total number of frames to be used and the time range (in ns) corresponding to the selected frames are shown to the right of the button. Opens the Trajectory Frames dialog box, in which you can set the following:

  • Frame range text boxes—Set the range of frames to use. You can also use the slider to select the range.
  • Step size text box—Set the interval at which trajectory frames are taken. For a step size of n, every nth frame is taken within the selected range. The first and last frames are always included. Increasing the step size decreases the number of frames to be used and the computational time needed.
  • Frames text—Lists the corresponding frame numbers of the selected frame range and step size.
  • Time text—Lists the corresponding time range and interval (in ns) of the selected frame range and step size.
  • OK button—Apply the selected trajectory frame range and step size and close the dialog box.
Transference ion menu

Select the cation species to use as the transference ion. If you select a polyatomic species, you must use the Select Atom option to choose which atom within the molecule should be treated as the "transference ion" for the purposes of the calculation.

Select Atom option

Click on this option after selecting a polyatomic species from the Transference ion menu. In the Workspace, pick an atom on one of the molecules of the polyatomic species. The atom you picked is representative of what is used as the "transference ion" for which coordination is calculated in all the molecules of the polyatomic species in the system. The name of the selected atom appears as text to the right of the Select Atom option.

Only present if a polyatomic species is selected as the Transference ion.

Counterion menu

Select the anion species to use as the counterion.

Coordination element menu

Select coordination elements from the chosen counterion. The coordination of the selected elements with the transference ion is calculated when the job is run. All elements in the species selected in the Counterion menu except for C and H are displayed in the Coordination element menu. Multiple elements can be selected.

Chain coordination element menu

Select coordination elements from any species that is not the transference ion or counterion. All elements in those species except for C and H are displayed in the Chain coordination element menu. Multiple elements can be selected.

Coordination cutoff text box

Enter the maximum coordination distance between transference ion and coordination elements, in angstroms.

Visualization cutoff text box

Enter the size of the coordination sphere around the transference ions for the visualization, in angstroms.

Combine coordination shells for nearby transference ions option

Select this option to merge the coordination shells of transference ions that are within the coordination cutoff of each other into a single cluster. When selected, all analysis in the Electrolyte Analysis Viewer Panel, except for Structural Analysis, uses these combined cluster definitions.

Calculate RDF for transference ion element option

Select this option to calculate the radial distribution function (RDF) between the selected atom of the transference ion and all coordination elements.

Generate density isosurface option

Select this option to calculate the density isosurface of the selected Transference ion with respect to the center of mass of the selected Counterion. Set parameters for the isosurface calculation using the Advanced Options button.

This option must be selected to view the Density Isosurface results in the Electrolyte Analysis Viewer Panel.

Calculate structure factor option

Select this option to calculate the structure factor S(q) from the RDF data. Only available when Calculate RDF for transference ion element is selected.

Advanced Options button

Set parameters for RDF, isosurface, and structure factor calculations. Opens the Advanced Options dialog box.

RDF resolution text box

Specify the bin width for the RDF calculation, in angstroms. Only available when Calculate RDF for transference ion element is selected.

RDF max distance text box

Specify the maximum distance for the RDF calculation, in angstroms. Only available when Calculate RDF for transference ion element is selected.

Isosurface cutoff distance from options

Select which cutoff distance to use for the density isosurface. Select RDF to use the distance from the first peak of the RDF function. Choose Coordination to apply the value specified for the Coordination cutoff. Only available when Calculate RDF for transference ion element is selected.

Isosurface resolution text box

Specify the grid resolution, or space between the grid points, when calculating the isosurface, in angstroms. Only available when Generate density isosurface is selected.

Number of waves in each dimension text box

Specify the number of waves in each dimension for the structure factor S(q) calculation. Only available when Calculate structure factor is selected.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Electrolyte Analysis Calculations - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

Use the Reset button to reset the panel to its default settings and clear any data from the panel. If the panel has a Job toolbar, you can also reset the panel from the Settings button menu.

If you can submit a job from the panel, the status bar displays information about the current job settings and status for the panel. The settings include the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

The status bar also contains the Help button , which opens an option menu with choices to open the help topic for the panel (Documentation), launch Maestro Assistant, or if available, choose from an option menu of Tutorials. If the panel is used by one or more tutorials, hover over the Tutorials option to display a list of tutorials. Choosing a tutorial opens the tutorial topic.

Tutorials

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