Avoid cd-ing to directories

[ijpulidos]

For bash scripts and all the scripts in general it's a good idea to avoid changing the directory in the script (avoid cd command). Specifically the script do_pca.sh does this. I think it is because of a gromacs limitation, since it doesn't allow to specify paths for all the outputs to not clutter the current working directory where the script is called from... but have to check and fix if possible.

This is in order to try to avoid using absolute paths in the parameters/flags when using these scripts.