[gmx-users] g_anaeig

barrett barrett at biop.ox.ac.uk
Fri Aug 6 14:02:20 CEST 2004


I have been using g_anaeig with -extr to generate a range of structures.
As you know the set is centered on an average structure and contains
configurations extrapolated along a given eigenvector.

I can do this for the first two eigenvectors, and I get two sequences.

What I would really like to do now is generate a single matrix of
structures as follows

Structure(x,y)=average structure + (x*eigenvector1) + (y*eigenvector 2)

Where x and y are in the range -2,-1,0,1,2 (or some scaled equivalent).
Looking at it this way the current output of

g_anaeig -extr -first 1 -last 2 etc

is simply the central row and central column of my matrix : [(-2:2),0]
and [0,(-2:2)]. I want [(-2:2),(-2:2)]

a)     Am I right in thinking that g_anaeig cannot yet do this 2
eigenvector scan.
b)     If so: I have looked at the source code for g_anaeig and am
rather daunted to fiddle with it. If anyone would be interested in
implementing this scan I would be very interested to try it. (Cheeky, I
c)     Otherwise I think Im going to have to extract the eigenvector
data from eigenvec.trr and make up my own analysis.

Any (polite!) comments welcome.


Dr Paul Barrett


Laboratory of Molecular Biophysics
Department of Biochemistry
University of Oxford

Tel 01865 275369
Fax 01865 275182

 <mailto:barrett at biop.ox.ac.uk> barrett at biop.ox.ac.uk
 <mailto:hellopaul1 at hotmail.com> hellopaul1 at hotmail.com

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