[gmx-users] about how to create covar.ndx for dihedral Principal Component Analysis

[lazaro monteserin]

Dear Gromacs users,

I am trying to run a dPCA to select the best conformation from my
trajectory.

When I follow the steps in gromacs manual I have a question about one of
the steps:

3. Make an index file
<http://www.gromacs.org/Documentation/File_Formats/Index_File>, named as
covar.ndx, which necessarily contains one group of atom 1 to
integer(2*N/3), where N is the number of dihedral angles. For example, for
a peptide of 5 dihedral angles

How can I create the covar.ndx? How could I use gmx make_ndx for this?

In my case I have 99 atoms and 66 cos/sin integrals. So I guess the
covar.ndx should has one group with atoms numbers from 1 2 3 4 5... to 66?

Should I have to do this in a text editor by hand?

Kindly,

Lazaro