VMD-L Mailing List

From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Fri Aug 27 2010 - 13:06:40 CDT

Dear VMD users,

I have a question about RMSD trajectory tool on VMD.

In options menu, if I select "protein and resname ... and resid ... and atom x", the program calculates RMSD for "atom x" for all frames and also gives me the "avg" for RMSD as well. Does anyone know what equation is used by program to get RMSD for "an atom"? Is it actually just the atom deviation from the reference structure and not RMSD? I have actually written a script to get the atom deviation for each atom and the results differ from what is produced by RMSDTT so, I think I need to make sure the equation I am using is the same as VMD first.

Thanks,

Parisa