[gmx-users] Analysis of enssemble of MD trajectories

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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