[gmx-users] g_anaeig -proj

[chris.neale at utoronto.ca]

Carla: Agreed that this can be confusing.

What you seem to want can be obtained with g_anaeig -filt

Nevertheless, What you get with -proj can also be very useful.

For a very quick overview: -filt will output a .xtc file that contains  
only those motions that are along the selected EVs. Separately, -proj  
can project the trajectory down into an N-dimensional space for N  
selected EV's... I think that if you had followed the tutorial further  
and made the xmgrace plot (with both 1st and 2ns EVs) as the tutorial  
suggests, then you might have had a better chance to understand this  
part.

###

Tsjerk: First, great tutorial, I hadn't seen this before. Second, you  
might avoid this type of confusion by mentioning during the command:

g_anaeig -s ../topol.tpr -f ../traj.xtc -v eigenvectors.trr -eig  
eigenvalues.xvg -proj proj-ev1.xvg -extr ev1.pdb -rmsf rmsf-ev1.xvg  
-first 1 -last 1

that you care actually doing a few things at once... or perhaps  
actually break the command apart into separate g_anaeig -proj and  
g_anaeig -extr calls.

###

All: might it be a good idea to get the html addresses of nice  
tutorials into the output messages of the analysis tools?

Chris

-- original message --

Hi everyone,

please I'm doing for the first time a covariance analysis.
I followed this tutorial:
http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html<http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/analysis1.html>

But I don't understand. -proj gives the projection of the trajectory on the
first eigenvector, so I was expecting to have new coordinates for each atom
or each residue. Instead, I get a .xvg file saying:
""projection on eigenvectors (nm)"
@ xaxis  label "Time (ps)"
yaxis  label "vec 1"

Please can anyone tell me what this actually means? What data is in
nanometers? What does gromacs project?

Sorry if my question is stupid, but I can't find the answer.

Thank you.

Carla