[gmx-users] Dihedral Population Analysis -Index file

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Tue Jan 24 00:35:41 CET 2017

Dear Gromacs users,

I have a trajectory file which I wish to do a dihedral analysis for
specific dihedral.
Based on what I understood from mailing list and manual, I made an
index.ndx manually for the dihedral of interest in the molecule.

Usually, when we make an index file, say for atom P in the system, make_ndx
makes an index file which includes the numbers for all the P atom in the
system. These numbers are the index numbers in the .gro file for the whole

In my index file, I made it based on the atom numbers in the topology file
for the lipid.
For doing analysis, I first used trjconv and saved only the .xtc file for
only the lipid of interest, and then used g_angle to calculate the dihedral
population. I think what I get is only for ONE lipid over time NOT an
average over time and lipids in the system.

The obvious solution would be to include all the dihedrals for all the
lipids in it.
BUT, this is not easy to do manually. I tried mk_angndx but it is not
giving me what I want.
Is there any way to do this?

Thanks in advance for any comment and suggestion


*Rewards work better than punishment ...*

More information about the gromacs.org_gmx-users mailing list