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

Ali Khodayari ali.khodayari at student.kuleuven.be
Mon Apr 8 19:35:08 CEST 2019

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

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.



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