Surfactant Tilt Calculation Panel

Calculate tilt and rotational angles of surfactants from an MD simulation to evaluate orientation and alignment of surfactants.

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

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

  • Overview
  • Using
  • Features
  • Additional Resources

Overview of Surfactant Tilt Calculation

The tilt angle of a surfactant is the angle between the normal vector of a plane that represents the surface, and a vector from the surface to the hydrophobic end of the surfactant, which represents the orientation of the surfactant. The surface plane can be defined in different ways, for example, as best fit plane to selected atoms or orthogonal to crystal vectors. To define the rotational angle of a surfactant, the orientation vector is projected onto the surface plane. The angle of this projected vector with the x-axis is the rotational angle of the surfactant. The distribution of tilt and rotational angles shows if surfactants are aligned or unordered.

Using the Surfactant Tilt Calculation Panel

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

Surfactant Tilt Calculation Panel Features

Load from Workspace button

Load a structure from the Workspace into the workflow. Include a structure with an associated trajectory in the Workspace and click this button.

Trajectory Frames button

Set the range and interval of the trajectory over which the surfactant tilt angles are evaluated. 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.
Plane selector section

Define the plane to represent the surface against which the tilt angle of the surfactants is measured.

Best fit to selected atoms option

Define a plane from a fit to all selected atoms in the Workspace.

Crystal vector option

Define a plane that is orthogonal to the a, b, or c vectors of the simulation box.

Choose at least 3 atoms to define the plane option

Pick at least three atoms in the Workspace to define a plane that fits best to the selected atoms. Click on the Clear Selection button to clear the selected atoms in the Workspace.

Head/Tail selector section

Define the hydrophilic and hydrophobic parts of the surfactant. The hydrophilic part (“head”) defines the surface, the hydrophobic part (“tail”) defines the end point of the vector which is used to analyze the tilt angle.

Surfactant option menu and Group by button menu

Select the surfactant for which the analysis is performed. By default, the option menu is grouped by molecule type, given by the empirical formula. To group the option menu in a different way, click the Group by button to open a menu and select from:

  • Molecule— Choose to list molecules by Formula, SMILES, or Chiral SMILES.
  • Polymer— This may be useful for structures built with the Polymer Builder Panel. Choose to list polymers by Name and SMILES, or Name and Chiral SMILES.
  • Residue— This may be useful if the surfactant molecule is bonded in some way to a surface, and thus the entire system is formally a single molecule. The surfactant is then defined as a chain of residues of the given type attached to the head (hydrophilic) group. Choose to list residues by Formula, SMILES, or Chiral SMILES.

Hover over the Group by button to display a tooltip with the current selection.

Representative hydrophilic end atom indices text box and Pick option

Select atom indices representing the hydrophilic part of the surfactant. The plane in the Workspace shifts to the center of mass of the picked atoms.

Representative hydrophobic end atom indices text box and Pick option

Select atom indices representing the hydrophobic part of the surfactant. An arrow is drawn in the Workspace from the surface plane to the center of mass of the picked atoms.

Job toolbar

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

The Job Settings button opens the Surfactant Tilt Calculation - 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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