Distance, angle, and dihedral measurements

The Distances, Angles and Dihedrals tool measures geometric parameters along all the frames of a trajectory (molecular dynamics, scans, NEB, umbrella sampling windows, etc.). Several measurements can be defined at once; the results are shown as a table and as a plot, and can also be written to a log file.

To open the tool:

• Open the Main Menu.

• Go to Analysis.

• Select Distances, Angles and Dihedrals.

Defining the measurements

The atoms are chosen with the picking selection mode (Selection > Selection Mode > Picking). Click the atoms in the 3D view in order: they are labeled #1, #2, #3 and #4, as shown in the images below. Then click the corresponding button in the window:

• Distance #1 - #2: distance between atoms #1 and #2, in Å.

• Angle #1-#2-#3: angle formed by atoms #1, #2 and #3 (#2 is the vertex), in degrees.

• Dihedral #1-#2-#3-#4: torsion angle defined by the four atoms (rotation around the #2–#3 bond), in degrees.

Each measurement is added as a line of the list, showing its type and the index/element of the atoms involved (Figure 1). Repeat the procedure to add as many measurements as needed. To remove a line, select it and press Delete; Clear List removes all of them.

Running the analysis

• log file: the name of the output file (the .log extension is added automatically).

• Working Folder: the folder where the log file is written.

Click Run. The measurements are computed for every frame of the object that contains the picked atoms. The values are displayed in a text window (one line per frame, one column per measurement), written to the log file, and plotted as a function of the frame number. The plot window allows the image to be saved.