Diffusion Coefficient Viewer Panel

Diffusion Coefficient Viewer Panel Features

Use structures from option menu

Choose the structure source for the current task.

• Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries.
• Workspace (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries.

Open Project Table button

Open the Project Table panel, so you can select or include the entries for the structure source.

Load Data button

Load the data for the selected entries into the workflow.

Diffusion Parameters tab

Display values of diffusion coefficients and plots of the mean square distance (MSD) against simulation time difference. The fit of the MSD to obtain the diffusion coefficient can be adjusted.

Results table

This table shows the results for each structure that was loaded, giving the diffusion coefficients, the species identification, the method used for the fit, and the location of the data files.

Results plot

Plots the MSD against the simulation time differences tau, with controls for adjusting the fit of the MSD to calculate the diffusion coefficient.

Plot toolbar

This is a standard plot toolbar, described in the Plot Toolbar topic.

Plot area

Display a plot of the mean square displacement as a function of simulation time relative to the specified starting point.

The plot shows vertical blue dotted lines. These lines can be dragged in the plot area to adjust the limits used for the fit. The values in the fitting limit text boxes are updated as you drag the lines, and the diffusion coefficient is updated.

Diffusion coefficient text box

This noneditable text box reports the value of the diffusion coefficient.

Left fitting limit text box

Specify the lower time limit for fitting the linear portion of the graph to obtain the diffusion coefficient. The left blue line in the plot is adjusted when you change the value.

Right fitting limit text box

Specify the upper time limit for fitting the linear portion of the graph to obtain the diffusion coefficient. The right blue line in the plot is adjusted when you change the value.

Standard error/deviation text box

This text box reports the standard error in the fit for the mean square displacement method, the standard deviation of the fit for the velocity autocorrelation method. The values can be saved as Maestro properties.

Fitting parameters text boxes

These text boxes report the parameters of the fit: the slope, intercept and R² values for the mean square displacement method, the coefficient of variation for the velocity autocorrelation method.

Store Data button

Save the current value of the diffusion coefficient and errors as properties to the project entry.

Diffusion Trace tab

Display the trace of a selected object as it diffuses through the system, either as three 2D plots or a 3D plot. The trace is composed of the positions of the center of mass of the selected object, calculated for each trajectory frame and connected with straight lines. The center of mass of the selected objected is calculated from the mean square displacement. If the molecule crosses the cell boundary, the trace continues in the next cell. The plot axes represent the full range of movement in any of the Cartesian directions, and across cell boundaries. This tab is only available for entries that have Mean Squared Displacement (MSD) as their method.

Entry option menu

Choose the entry for which to display the trace. The menu contains the loaded entries that have Mean Squared Displacement as their method.

Mass center text box

Specify the index of the diffusing object to trace. The object is the one specified under Center of mass for diffusion parameters section in the Diffusion Coefficient Panel.

Plot type options

Choose an option for the type of plot.

• 2D—plot the trace projected onto the three planes, xy, xz, yz.
• 3D—plot the trace as a three-dimensional plot.

Highlight in workspace option

Select this option to highlight in the workspace the atoms corresponding to the object specified in the Mass center text box. Changing the Mass center automatically updates the atoms highlighted.

Plot toolbar

The toolbar has tools for manipulating the plot and for saving images. The buttons that are common to all plot toolbars are described in the Plot Toolbar topic.

Plot area

This area displays the plot for the choice of plot type. You can rotate the 3D plot using the left mouse button. Other actions are available from the plot toolbar.

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.

Related Topics

• Diffusion Coefficient Panel