Dear Justin, Thanks for your reply. Tsjerk: http://lists.gromacs.org/pipermail/gmx-users/2009-October/045884.html
There are two things to distinguish: > > 1. The reference structure used to remove translational and rotational > degrees of freedom > 2. The reference against which the deviations (on a per atom base) are > calculated that are then squared, averaged and taken the root of (root > mean square fluctuation). > > These two need not be the same. It is common, and most sensible, to > calculate the deviations against the average structure, after fitting > all structures in the trajectory against a certain reference > structure. With option -od the deviations against the reference used > for fitting are calculated rather than against the average. You do > need a reference for fitting, since otherwise you include overall > rotation and translation in the calculation of the RMSF, which you > usually wouldn't want. > 1.) For RMSD, You said (i.e. the one present in the .tpr file). which one? How do Gromacs select the reference structure? 2.) Tsjerk: RMSF calculate the deviations against the average structure, after fitting all structures in the trajectory against a certain reference structure. the reference structure is taken as average over the trajectory. That is, it is the average structure (please look at example). isn't it? *For example:* coordinates of N atom: x y z 2 4 6 8 7 1 8 1 2 the average structure of N atom:[(x1+x2+x3)/3, (y1+y2+y3)/3, (z1+z2+z3)/3]. isnt it? x y z 6 4 3 3.) This "The reference structure used to remove translational and rotational degrees of freedom" is RMSD??? 2011/9/21 Justin A. Lemkul <[email protected]> > > > ahmet yıldırım wrote: > >> Dear users, >> >> g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res >> >> With the option -od the root mean square deviation with respect to the >> reference structure is calculated. >> Then, >> RMSDEV is the RMSD per residue (the root mean square deviation with >> respect to the reference structure is calculated). >> >> and >> RMSF is the RMSD per residue (the root mean square fluctuation (RMSF, i.e. >> standard deviation) of atomic positions after (optionally) fitting to a >> reference frame). That is, it is the measurement averaged over all atoms in >> each residue. >> >> Now what difference? >> >> > The RMSD is measured relative to the reference structure (i.e. the one > present in the .tpr file). RMSF is measured with respect to average > coordinates. > > -Justin > > > I am confused. >> >> -- >> Ahmet YILDIRIM >> >> > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Ahmet YILDIRIM
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