[gmx-users] Analysis of enssemble of MD trajectories

[francesco oteri]

Hi,

2012/9/21 James Starlight <jmsstarlight at gmail.com>

> 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 <lloyd.riggs at gmx.ch>:
> > 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 <jmsstarlight at gmail.com>
> >> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >> 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
> >> --
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-- 
Cordiali saluti, Dr.Oteri Francesco