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

[ZHANG Cheng]

Dear Justin and Peter,
Thank you sooooooooo much! I did not realise the meaning of two prompts until now. I was always using the same number for the two prompts.


Thank you for the MDAnalysis!
https://www.mdanalysis.org/pages/learning_MDAnalysis/


Yours sincerely
Cheng




------------------ Original ------------------
From:  "ZHANG Cheng";<272699575 at qq.com>;
Date:  Fri, Nov 24, 2017 06:25 PM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;

Subject:  Re: Does RMSD only consider the "relative" coordinate changes for the selected group?



Dear Justin,
Thank you for confirming this. May I ask,


1) How to "fit to the whole protein (or backbone, CA, etc) and subsequently calculate the RMSD of given residue(s)"?


My current command is (by selecting the residue in the "index.ndx" file):
gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ns


2) Is there a tutorial/manual for using python to extract coordinates at customised time and group?


I will look at the "gmx traj -ox".


Yours sincerely
Cheng




------------------ Original ------------------
From:  "ZHANG Cheng";<272699575 at qq.com>;
Date:  Fri, Nov 24, 2017 00:20 AM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>;
Cc:  "ZHANG Cheng"<272699575 at qq.com>; 
Subject:  Does RMSD only consider the "relative" coordinate changes for the selected group?



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