[PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

[sunyeping <sun...@al...>]

Dear everyall,

I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames and a reference structure (B.pdb) into pymol. I wish to get the rmsd value between each state of the MD simulation trajectory and the reference structure, but I don't know how. I can use the align command as: "align A, B", but this only gives one rmsd value. Could you tell me how to get the rmsd value between each state of the MD simulation trajectory and the reference structure?