[gmx-users] Dihedral PCA documentation

[Anna Lappala]

Dear Gromacs users,

The documentation on Dihedral PCA analysis is confusing.

 Firstly, the links are redirecting to the main gromacs page which does not help because one needs to search for the specific commands from there. 

Secondly, -s option does not work in step 2: invalid command line argument "-s". 

Thirdly, my tpr file contains water which I do not want to include in the analysis, how can I change that?

.ndx file output produced by mk_angndx is a mess- first line, for example, is [UB_th=108.4_297.062f] 

I need a small number of dihedrals, so I could write the file myself but there again is no clear explanation how to do it: the [foo] 1 2 3 4 example could be expanded- do I use "dihedrals" instead of foo? Or filename? Or molecule name? 

Finally, I would really appreciate it if someone could give an explanation or a clear example of how this works, for a simple system or a protein, because documentation is unclear to me.

Kind regards,
Anna