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";<272699...@qq.com>; >> Date: Fri, Nov 24, 2017 00:20 AM >> To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; >> Cc: "ZHANG Cheng"<272699...@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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