[gmx-users] Analysis of enssemble of MD trajectories

James Starlight jmsstarlight at gmail.com
Thu Sep 20 12:06:40 CEST 2012

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?


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