[gmx-users] Combined essential dynamics

Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl
Fri Aug 27 12:25:06 CEST 2004

Hi Ram,

Since you only use frames from 1ns - 5ns from the simulation, you'll 
miss the identical projections the starting structures would give. If 
you want to know how your individual trajectories run in the plane 
defined by these two eigenvectors, project the whole trajectories. Both 
projections should indeed start from the same point if the starting 
structures are identical.



Sekar Ramachandran wrote:

>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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