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

[Justin Lemkul]

On 11/24/17 5:25 AM, ZHANG Cheng wrote:
> 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

You're prompted for two groups: one for the fit and one for the RMSD 
calculation. In that case, refer to what I said before (because I said 
it in a specific order for a reason :)

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

No.

-Justin

>
> 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

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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