[gmx-users] order of atoms in the index file

[Ali Khodayari]

Hello all,

I am trying to calculate the dihedral angels of a group of atoms in a
molecule. As I am only interested in part of the molecule, I have manually
made an index file containing  the desired atoms in groups using gmx
make_ndx. 

Yet, the atom's number in each group is in ascending order. Means that
instead of having orders of 858 855 875 865, as expected, I get 855 858 865
875. Is there any way to fix the order of atoms based on selecting procedure
while the index file is being made? Obviously it has a great difference on
the calculation of dihedral angles.

P.S. I am not using gmx mk_angndx as there are dihedral similarities in the
system, and I need to exclude them.

Regards,

Ali