[gmx-users] Analysis of enssemble of MD trajectories

Justin Lemkul jalemkul at vt.edu
Thu Sep 20 12:08:26 CEST 2012

On 9/20/12 6:06 AM, James Starlight wrote:
> 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?

I think what you want is not concatenation, but rather simultaneous display. 
Analyze each trajectory separately and simply plot the data in one graph, i.e. 4 
different RMSD traces in one panel.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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