Trajectory Density Analysis Panel

Generate density profiles and cross-sections from the frames of a trajectory that can be averaged over a range of the trajectory. The methods are similar to that used in the Density Profile Panel.

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

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

  • Using
  • Features
  • Additional Resources

Using the Trajectory Density Analysis Panel

The input to this panel is the trajectory from an MD simulation. The analysis works best for simulations with constant volume, i.e. run in the NVT ensemble. Although it is possible to use a simulation in the NPT ensemble, the lack of constant volume presents difficulties in averaging over the trajectory and hence can result in artifacts in the density at the edges of the simulation box if the volume fluctuation is not very small.

To visualize the results of the calculation, you can use the Trajectory Density Analysis Viewer Panel (click the Tasks button and browse to Materials → Classical Mechanics → Trajectory Analysis → Trajectory Density 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 trajectory_density_analysis_driver.py Command Help.

Trajectory Density Analysis Panel Features

Load from Workspace button

Load the trajectory associated with the structure in the Workspace. The title of the Workspace structure is shown next to this button when the trajectory has been loaded.

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.
Atom group selection tool sets

Specify groups of atoms for density analysis. Each group is analyzed separately and can be visualized separately. This feature allows you to examine the density of different parts of the structure, such as the two layers in a bilayer, surfactant micelles, or different components of a polymer mixture.

Multiple groups can be specified by adding tool sets with the Add Atom Group button. Each tool set has the following tools:

tool set management buttons

These buttons perform display and ordering operations on the tool set. They allow for easy duplication and rearrangement of tool sets.

    Show or hide the contents of the tool set. When hidden, only the tool set number, label (if any) and these buttons are displayed. This is useful when you have a number of tool sets and want to compare two separate tool sets, for example.
    Move the tool set up or down one place in the list.
Duplicate the tool set. This is useful for creating similar tool sets with variations on the settings.
Delete the tool set.

Selection name text box

Enter a name for each atom group to be selected in the Select atoms for density analysis section in this text box.

Select atoms for density analysis section

This section contains a standard set of picking tools that you can use to select a group of atoms for density analysis.

Center trajectory on this selection option

Center the trajectory on the centroid of the atoms of this group. When you select this option, it is deselected in any other group if it is already selected there.

Centering the trajectory on a group of atoms eliminates drift of the structures across the cell, which would smear out the time-averaged density in the drift direction.

Add Atom Group button

Click this button to add another selection tool set at the end of the list.

Custom slice thickness option and text box

Set the slice thickness for the density profile, in angstroms. The default is determined automatically, depending on the simulation box. This option allows you to choose an approximate slice thickness. The thickness you supply is adjusted to the nearest value that results in an integer number of slabs in the box, and the updated value is reported in the log file.

Calculate density isosurface option

Compute the density isosurface for the specified groups of atoms. Density is computed by dividing the mass of the specified atoms in the slabs by the volume of the respective slabs.

This option must be selected to view the Density Isosurface tab of the Trajectory Density Analysis Viewer Panel.

Job toolbar

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

The Job Settings button opens the Trajectory Density Analysis - 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

Related Topics