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Dear all i try to êrform PCA for protein-ligand complex in google colab pro by runnig this command echo 3 22| gmx covar -f md_0_100_fit.xtc -s md_0_100.tpr -n index.ndx -o eigenval.xvg -xpm covar.xpm -b 50 -e 100 -tu ns
3 C alpha
22 Protein_UNL
when i open the output file covar.log i fount that the covariance analysis was performed just from 50ns to 67.79ns may i know what is the potential problem
Thanks in advance