[gmx-users] Does RMSD only consider the "relative" coordinate changes for the selected group?

[ZHANG Cheng]

Dear Gromacs,
When I calculate the RMSD for the whole protein, I got values mostly from 0.2-0.5 nm. However, when I only calculate for a particular residue (using an index file), the scale is mostly only 0.01-0.02 nm, even for a residue on the loop.


My understanding is: when doing the RMSD, the software will align the selected group to the group in the reference, as much as possible. Then the software calculates the root mean square deviation.


As a result, though a protein may deviate a lot from its reference structure, if only one residue is selected for RMSD, the relative positions of the atoms within that residue still remain almost the same relative coordination, which makes their RMSD only 0.01-0.02 nm.


Can I ask if my understanding is correct?


I wonder, if I can write some script (e.g. python) to manually extract the coordinates information from various frames in the xtc/trr file?


Thank you.


Yours sincerely
Cheng