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";<272699...@qq.com>; Date: Fri, Nov 24, 2017 06:25 PM To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@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";<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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
