Hi Michael, g_rms should do the trick. First create an index file having an atom group identical in both systems. Then, g_rms -s ref.pdb -f1 trj1.xtc -f2 trj2.xtc -m rmsd.xpm gives you an rmsd matrix with entry ij given by RMSD[(frame i of trj1),(frame j oftrj2)]. The diagonal of that matrix should be what you want.
Marcus Michal Kolinski wrote: > Dear Users, > > I've created two different models of the same > transmembrane protein. These two models were > created using homology approach using two different > templates (both with similar sequence similarity > to the sequence of the target protein). Next, I > did two separate 25ns simulations of those two > obtained protein models in water and lipid environment. > RMSD value calculated using g_rms reaches about 3.5 A > after 10 ns in two simulations and stays stable for > the rest of the MD time. > > What I want to do is to obtain a plot of RMSD > between those two models (model one vs model two) > for each corresponding frame of those two MD simulations > (I just want to add that the length of protein chain is > different in both protein models). Is there a script > available from gromacs tools which could be used for this? > Could you give me some sugestions how to treat this problem? > Thank you in advance. > Michal > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- Dr. Marcus Kubitzki Max Planck Institute for Biophysical Chemistry Computational Biomolecular Dynamics Group Am Fassberg 11 D-37077 Göttingen Germany phone: ++49-551-2012312 fax: ++49-551-2012302 Email: mkubitz[at]gwdg.de www: http://www.mpibpc.mpg.de/groups/de_groot/ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
