Hi, 2012/9/21 James Starlight <[email protected]>
> Dear collegues > > Thank for advices. Indeed Gromacs is able to analyse two trajectories > with g_rms ( with the flags -f and -f2 ) but as the result I've obtain > graph with one rmsd plot so I'm not sure about implementation of that > method. > In this case it computes the n1*n2 rmsd matrix! Each frame of the first trajectory is compared with the second trajectory. > > So I think that the algorithm proposed by Justin was exactly what I > need. But I'm not sure also how I could do such ploating of results of > the different g_rms analyses to one common graph ( when I analyse new > trajectory and save it by the -o result.xvg if the result.xvg was > already exist the old graph is back up to the #result.xvg# etc ). > > James > > 2012/9/20 lloyd riggs <[email protected]>: > > Dear Dr. > > > > I might be wrong, but I think you can use g_rms with two seperate trj > files, and it takes the rms from the starting structure of the first one. > In which case you would have to decide which is the reference, and then > just do it three times. > > > > Theres also auxiliarry software which has plugins for this, such as VMD, > Pymol, or even O run in some sort of batch. In pymol I know it can be run > as a script, but you need all saved pdb files extracted from each trj, so > would be a bit large and pain. with the VMD it has plugins for them, but I > only played with it once. If you only want to look at beginning and end > rms from say the start and end for all traj-using just a couple pdb at > either end would be easy in pymol and O. > > > > There is also these new tools I found in Bio R (its called Bio3D if you > look on the web for the freeware) , which are all scripts that I tried > once, which work as well, mostly the take a reference structure and parse > the pdbs output from a trj (if you write out each individually) but there > values are different but directtly correlatable (ie say 1.6 from the former > and something like 80% is cranked out by the later Vs 0.4 and 5% meaning no > change) > > > > Hope that helps, and if I am wrong about something somone corrects me. > > > > Stephan Watkins > > > > -------- Original-Nachricht -------- > >> Datum: Thu, 20 Sep 2012 14:06:40 +0400 > >> Von: James Starlight <[email protected]> > >> An: Discussion list for GROMACS users <[email protected]> > >> Betreff: [gmx-users] Analysis of enssemble of MD trajectories > > > >> Dear Gromacs Users! > >> > >> > >> I'm working with the enssemble of the MD trajectories calculated for > >> the common protein with the differences in the initial conditions in > >> the case of each trajectory. > >> > >> Now I'd like to perform analysis of that enssemble of data. For > >> example I'de like to obtain RMSD as well as RMSF graphs calculated > >> from all trajectories in one common graph for comparison of the > >> dynamics of the systems. > >> > >> I've used trjcat on my 4 trajectories to obtain one merged trajectory > >> multi.xtc and than tried to calculate RMSD for that multi.xtc but the > >> resulted graph was wrong. > >> > >> trjcat -f md_150ns.xtc md_320ns.xtc sd_125.xtc sd_75ns.xtc -cat -tu ps > >> -o multi.xtc > >> > >> Is there any other way to do such analysis of several trajectories in > >> common graph? > >> > >> > >> James > >> -- > >> gmx-users mailing list [email protected] > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> 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 > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > 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 > -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
