RMSD is an abbreviation for root mean squared. The RMSD is a measure of the average distance between the atoms of a stacked protein (usually the backbone atoms). RMSD calculations can be applied to other non-protein molecules, such as organic small molecules. In studies of spherical protein conformations, the RMSD of the Cα atomic coordinates after optimal rigid body stacking is usually used to measure the similarity of the 3D structure. It is defined as follows:
where xi and x'i are the x-coordinates of the i-th atom of the two molecules.
An important prerequisite for calculating the RMSD between two molecules is to place the two molecules to the position with the greatest overlap, otherwise the calculated RMSD is meaningless, as shown in the figure below, where the two molecules are placed more randomly and at a larger distance, when the calculated RMSD will be large.
Make an input file and write the coordinates of the two molecules sequentially to the same xyz file
O -2.63 -1.82 0.10
H -1.67 -1.82 0.10
H -2.95 -0.92 0.10
O 0.12 -1.36 0.19
H 1.08 -1.36 0.19
H -0.19 -0.46 0.19
The first half of this file is the standard way to write an xyz file for a water molecule, the first line is the atomic number, the second line is the title or description of the molecule, the content is arbitrary, the third line onwards is the coordinates, the format is the element symbol plus the coordinates or the atomic number plus the coordinates, for example in the above file O can be replaced by 6 and H by 1. Drag the file into the VMD Main window and you can see that only one structure is displayed. You can switch to another structure by dragging the slider at the bottom.
If you want to display both structures at the same time, you can set in the Graphics → Representations option.
In the Draw style option, choose Trajectory → Timeste for the Coloring Method, then go to the Trajectory tab and write 0:1 in Draw Multiple Frames, so that both structures can be displayed at the same time.
To start the RMSD calculation below, select Extensions → Analysis → RMSD Trajectory Tool in the VMD Main window to open the RMSD window. Change Protein to all in the upper left dialog box and remove the check mark in front of noh (indicating that hydrogen is not considered) at the bottom. On the right side there are two key buttons RMSD and ALIGN, we first try to not ALIGN, at this time the RMSD value is 3.319 Å, as shown in the following figure.
Finally, let's export the image and review some simple operations of VMD plotting by the way.
Remove the axes at the bottom left: Display → Axes → Off
Change the background to white: Graphics → Colors, choose Display in Categories, then choose Background in Names, and finally choose 8 white in Colors.
Save the image: File → Render