[gmx-users] Principal Components Analysis in Gromacs

Thomas Evangelidis tevang3 at gmail.com
Wed Mar 28 15:20:52 CEST 2012

Hi Tsjerk,

Thanks for all the clarifications about PCA you make on the mailing list! I
have a question about the commandlines you wrote. Why do you use the .tpr
file with the "-s" flag? Is it because you want to compare the
mass-wheighted covariance matrices? I use to calculate the covariance
matrices by giving to g_covar a .pdb file with the "-s" flag and then
calculate the RMSIP without giving any structure file. I guess no masses
are used in that covariance analysis, right? Do you recommend using atom
masses for PCA in general?

Thanks in advance for any help.

> - If you want to project the x-ray structures onto the eigenvectors
> from the MD simulations, you have to use
> g_anaeig -v eigenvec_from_md.trr -s reference.tpr -f xray_structures.pdb
> -proj
> - If you want to compare the similarity of the eigenvectors obtained
> from MD and from your crystal structures, you have to do PCA on both
> sets separately and then
> g_anaeig -v eigenvec_from_md.trr -v2 eigenvec_from_xray.trr -eig
> eigenval_from_md.xvg -eig2 eigenval_from_xray.xvg -s reference.tpr
> -inpr



Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/
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