Calculation Principal Component analysis (PCA)

User discussions
1

GROMACS version: 2018
GROMACS modification: Yes/No no
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Dear GROMACS users

I need to investigate the effects of a duplication mutation in my protein structure and function. It is needed to calculate protein motion and free energy landscape analyses.
issued this command to calculate eigenvec.trr and eigenvalue.xvg
gmx covar -f nopbc.xtc -s .tpr
and now I want to compute PCA but I don’t know the exact
“gmx anaeig” command I should use.
I would be really grateful if someone can help me to understand and calculate it.

Thanks in advance
Farial

2

You can try along the following lines:
gmx_mpi covar -f out.xtc -s md.gro -n index.ndx -ascii -v eigenvec.trr -tu ns -last 2
gmx_mpi anaeig -v eigenvec.trr -f out.xtc -s md.tpr -proj pc1.xvg -first 1 -last 1 (replace 1 with 2 from 2nd eigenvector)

thank you

3

Dear Georgian

Thank you for replying

I issued these commands to calculate the covariance matrix:
gmx covar -f nopbc.xtc -s .tpr

and then issued this command to obtain 2dproj.xvg
gmx anaeig --v eigenvec.trr -f nopbc.xtc -s .tpr -eig eigenval.xvg -sd 2dproj.xvg -first 1 -last 2

is that wrong?

4

you didn’t mention the last PC to be consider by using the "-last " flag as the command above -last 2 was used meaning only the first two PCs will be in the output files.