Is there a size limit on the covariance matrix in

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1

Hello there

I am trying to do PCA on a large structure.
The covariance matrix is of size (85122x85122).
The “gmx covar” command runs fine but the expected output “-v eigenvect.trr” is not generated.
There is no error/warning…
The full command used is: gmx covar -s md.tpr -f md.xtc -o eigenval.xvg -v eigenvect.trr -xpma covara_mdfit.xpm -l covar.log

Any help will be appreciated
GROMACS version: 2021.1
GROMACS modification: Yes

2

Hi,

I suggest to consider whether a reduced set of atoms will meet your needs. Note that the diagonalization of a matrix requires memory and time that will increase at least as fast as than the square of the number of atoms involved.
You do not get error probably because gmx covar is not yet ready, but this can take very very long time.

Best regards
Alessandra