RMSD tool

In molecular dynamics (MD), the RMSD (Root-Mean-Square Deviation) is a widely used metric to quantify structural differences over time between molecular conformations.

Concept

The RMSD measures the average squared deviation between corresponding atomic positions in two structures (typically a reference structure and a trajectory frame).

The formula is:

To open the tool:

• Open the Main Menu.

• Go to Analysis.

• Select RMSD tool.

Selecting the atoms

Before running, select the group of atoms to be compared using the viewing selection mode (for example, the backbone of a protein or the heavy atoms of a ligand). All selected atoms must belong to the same object (trajectory).

Options (Figure 1)

• Frames from / to: the range of frames to analyze. The default (0 to -1) uses the whole trajectory; -1 means "until the last frame".

• Step Size: analyze one frame every n frames (default: 1, all frames).

• Reference – Frame: the frame used as reference structure (default: 0, the first frame).

• Reference – Use Average: uses the average structure of the trajectory as the reference instead of a single frame.

• Superpose each frame on the reference (Kabsch): before computing the RMSD, the selected atoms of each frame are fitted onto the reference (optimal rotation and translation), so that overall motions of the molecule do not contribute to the RMSD. Turn this option off only if the trajectory has already been aligned on the same atoms (see Align Trajectory).

• Plot the result: shows the RMSD (Å) as a function of the frame number. The plot also reports the number of atoms used, the reference and the mean RMSD, and can be saved as an image.

Click Run. The RMSD of each analyzed frame, in Å, is listed in a text window, and plotted if the corresponding option is active. Examples of RMSD curves are shown below.