[gmx-users] Combined essential dynamics

Sekar Ramachandran sram18 at yahoo.com
Thu Aug 26 20:54:12 CEST 2004

I am trying to carry out a COMB_ED analysis of two
forms of the  protein. I have carried out 5ns
simulations of the two proeins. I want to use 1 ns to
5ns data from the two trajctories to run an essential
dynamics analysis. I created a tpr file for both
protiens containing only the CA atoms. I concatenated
the two trajectories using the folloing command:
trjconv -f protein1.trr protein2.trr -o comb.trr
I set the firsttime as zero (it was 1 ns int he
original file).
on the prompt for last time : I entered c. I obtained
a trajectory file with 8 ns of data.
I ran g_covar on this with the following command:
g_covar -f comb.trr s protein1.tpr -o eigenval.xvg -v
I ran g_anaeig using the above eigenvectors and the
indivdual trajectories to obtain projections of the
indivdual trajectories of the two forms onto the first
two eigenvectors.
g_anaeig -v eigenvec.trr -f protein1.trr -s
protein1.tpr -2d 2dproj.xvg -b 1000 -e 5000 -first 1
-last 2.
When  I look at the 2D projections of the two
trajctories, they seem to be really far apart form
each other. This seems to be odd because the starting
structures for these forms are almost identical and  I
would have expected that at the beginning of the
simulations the two projections would be close to eact
other. (the rmsd between the two starting structures
is 0.0 angstroms). This makes me believe that there is
something wrong with the way I ahve carried out my
analysis. I would be really grateful to anyone who cna
help me with this.
Thanks a lot and am really sorry about this elaborate

Sekar Ramachandran
Research Associate
316 Baker Laboratories
DEpartment of Chemistry and Chemical Biology
Cornell University
Ithaca 14853

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