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

[Peter Kroon]

On 24-11-17 13:48, Justin Lemkul wrote:
>
>
> 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
You can/should take a look at MDAnalysis. But you shouldn't need it for
a RMSD.

Peter

>
>>
>> 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
>