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.
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
