Hi Alessandra,
Thank you for the reply.
I use the command “gmx covar -s md.tpr -f md.xtc” for calculating the covariance matrix. The system consists of a protein in a cubic box with tip3p water model.
It works if I run the same command on supercomputer where the production MD was performed but not on my personal system.
Kindest Regards
Purvi Gupta