Radial Distribution Function Panel
Calculate and plot radial distribution functions from a molecular dynamics simulation.
To open this panel, click the Tasks button and browse to Materials → Classical Mechanics → Trajectory Analysis → Radial Distribution Function.
- Using
- Features
- Additional Resources
Using the Radial Distribution Function Panel
The radial distribution function (RDF) gives the probability of finding a particle at a distance r from another particle. It is also known as the pair distribution function. The function is calculated from a trajectory as a histogram, in which bins are created for each distance range, and the count of interparticle distances that lie in the range for each bin are accumulated from each frame of the trajectory. The results are then normalized to give a probability.
Radial distribution functions are usually zero at small distances because of interatomic repulsion at these distances. There are often sharp peaks at distances that correspond to structure in the system: for example, the first solvation shell of a molecule in solution. The integral of the radial distribution function can provide information about average coordination numbers.
This panel allows you to calculate the radial distribution function for particles of the same type, or between two types of particles. A particle can be either an individual atom, or the center of a selection of atoms in molecules or residues.
The calculation requires a trajectory from a simulation. Once you have loaded the simulation file, you can specify the two atom sets and calculate the RDF. You can restrict the range of frames used from the trajectory (Crop Trajectory), set the bin size and maximum distance (Options), and make some choices for the appearance of the plot.
When the job has run, you can import the results and display a plot of the radial distribution function in the View Results tab. You can export an image of the plot, or export the data (function and integral) to a text file.
You can calculate the RDF for a trajectory directly by using the Plot button in the Trajectory Player.
You can also generate radial distribution functions from the command line—see Desmond Utilities.
Plot Radial Distribution Function Panel Features
- Run Calculation tab
- Trajectory source option menu
- Load button
- Import button
- Crop Trajectory link
- Atom Selection section
- Positional resolution text box
- Max distance for RDF text box
- View Results tab
- Status bar
- Trajectory source option menu
-
Specify the source of the trajectory for calculation of the radial distribution function:
- Workspace (included entry)—Use the entry that is currently included in the Workspace. Only one entry must be included in the Workspace. When this option is selected, the Load button is displayed.
- File—Read the structure from a file. When this option is selected, the Import button is displayed. The allowed file types are: Desmond CMS.
- Load button
-
Load the trajectory from the
- Import button
-
Click Import and in the file selector, navigate to the file you want to use for the trajectory. Upon the import, the structure is incorporated into the entry list and displayed in the Workspace.
- Crop Trajectory link
-
Set the range of trajectory frames to use when calculating the radial distribution function. Opens the Trajectory Filter dialog box, in which you can select the time range (in ns) using the text boxes or the slider.
- Atom Selection section
-
In this section you can specify one or two sets of atoms for which you want to calculate the radial distribution function. The Group by option menu, Calculate using option menu, and Atom selection query picking tools are common features to both Set 1 and Set 2 atom selections.
- Group by option menu
-
Choose how to group the selected set of atoms in the calculation. If Molecules or Residues is selected, the center of the selected atoms in each group is calculated and the pair correlation function is calculated between the centers instead of the individual atoms. For example, if the ASL expression for Set 1 is water, and Molecules is selected, the pair correlation function between the specified centers of all water molecules is calculated. The center is determined with the method selected from the Calculate using option menu. Atoms are not grouped by default.
- Calculate using option menu
-
Select how centers should be calculated if selected atoms are grouped.
-
- Center of Mass—use the center of mass to determine the center of each molecule or residue.
- Center of Charge—use the center of charge to determine the center of each molecule or residue.
- Center of Geometry—use the geometric center (centroid) without mass weighting of each molecule or residue.
-
Only present when the Group by option menu is set to Molecules or Residues.
- Atom selection query picking tools
-
Pick the atoms whose radial distribution function you want to calculate with picking tools and ASL. The ASL expression for the atoms is given (or can be entered) in the text box.
- Set 2 option
-
If you want to calculate the radial distribution (correlation) function for two different kinds of atoms, select this option and use the picking tools for the second set of atoms to pick the atoms. The ASL expression for the atoms is given (or can be entered) in the text box.
- Positional resolution (delta r) text box
-
Set the bin width for accumulating distance values, in angstroms. The calculation time increases as you decrease the bin width.
- Max distance for RDF (max r) text box
-
Set the maximum distance used for accumulating distance values, in angstroms. The calculation time increases as you increase the maximum distance.
- Import Results File button
-
Import the results of a radial distribution function calculation. The file that is selected is the log file (
.log) for the calculation. Opens a file selector so you can navigate to and select the file. - Export button
-
Export the radial distribution function to a plain text file or as an image in PNG, JPEG, or SVG format.
- Show integral option
-
Plot the integral of the radial distribution function on the plot as well as the function itself. The integral is evaluated at the same time as the function, so it is displayed immediately. You can use the integral to infer average coordination numbers.
- Display area
-
This area displays the function. When the integral is displayed, the axis on the right side is used to mark the integral values. The ASL expression is included in the title of the plot. Right-click on the plot to access a context menu, where you can save the plot as an image, export the function as a CSV or to Excel, or export all data as a
.datfile. - Status bar
Run Calculation tab
Specify the simulation for which you want to calculate a radial distribution function and set up the calculation. You can run the job using the Job toolbar.
View Results tab
View the radial distribution function and export it to a file.
The status bar displays information about the current job settings and status for the panel. The settings includes 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.
Use the Reset button 
to reset the panel to its default settings and clear any data from the panel.
The status bar also contains the Help button 
, which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a 
button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.