# PCA for Protein\_ligand complex **URL:** https://gromacs.bioexcel.eu/t/pca-for-protein-ligand-complex/7230 **Category:** User discussions **Created:** [September 20, 2023, 10:30am UTC](https://gromacs.bioexcel.eu/t/pca-for-protein-ligand-complex/7230 "2023-09-20T10:30:36Z") **Posts on this page:** 1 **Page:** 1
### Author: ![salwa](https://avatars.discourse-cdn.com/v4/letter/s/eb8c5e/32.png) [@salwa](https://gromacs.bioexcel.eu/u/salwa) #### Post date: [September 20, 2023, 10:30am UTC](https://gromacs.bioexcel.eu/t/pca-for-protein-ligand-complex/7230/1 "2023-09-20T10:30:36Z")
GROMACS version: GROMACS modification: Yes/No Here post your question 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