[gmx-users] g_anaeig

[barrett]

Hi

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
know!).
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.

Paul


Dr Paul Barrett

[**PLEASE NOTE NEW PHONE NUMBER**]

Laboratory of Molecular Biophysics
Department of Biochemistry
University of Oxford
Oxford
OX1 3QU

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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