[gmx-users] PCA

pawan raghav pwnrghv at gmail.com
Thu May 20 16:52:04 CEST 2010

I have a little concept problem regarding principal component analysis. So
my question is about ED sampling are as follows:

1. I have read from the manual that g_covar calculates and diagonalize the
(mass-weighted) covariance matrix. So what is the meaning of mass-weighted
in covariance matrix?

2. g_covar output the eigenval.xvg and and eigenvec.trr, but when I opened
the eigenval.xvg file it will shows nothing, i don't know what was wrong
with it?

3. what is the difference between covariance matrix and normal mode analysis
because both were used to generate the eigenval.xvg and eigenvec.trr file?

4. g_anaeig analyze the eigenvectors, so it is possible to fitted all the
structures generated at the time of simulations of single structure without
using the other structure?

I mean to say that it is possible to use single structure as initial to
simulate and ED sampling?

5. what is the need of eigenvec2.trr input file in g_anaeig to generate the
single number of covariance matrix as shown in manual? I have used to input
only one eigenvec.trr and eigenval.xvg, then it is right to do this?

6. I have used eigenval.xvg as input file in g_anaeig which do not shows
nothing when used to open in xmgrace. Then how this file used for generating
eigcomp.xvg, proj.xvg, eigrmsf.xvg, 2dproj.xvg, 3dproj.pdb (which I have
successfully generated).

7. One last question is related to g_analyze that it reads ascii file and
analyze data sets, but in actual it used some graph.xvg file as input. I am
confused about this graph.xvg file which file should I used for input to
calculate the cosine content of the principal components.

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