[gmx-users] Dihedral PCA documentation

Alex nedomacho at gmail.com
Tue Feb 28 00:04:33 CET 2017

I think you might be referring to the 2010 version of the online manual (
http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA), which is pretty
outdated. A lot of syntax seems to be changing fairly rapidly, so хрень
like this is to be expected. ;)
The current manual points to gmx angle, gmx covar and, gmx anaeig for
covariance analysis, and for those the updated help pages are separate:


On Mon, Feb 27, 2017 at 3:44 PM, Anna Lappala <lappala.anna at gmail.com>

> 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
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