[gmx-users] Dihedral transition times for a non-protein structure

Giulio Tesei giu.tesei at gmail.com
Tue Oct 4 15:50:53 CEST 2011

I'm performing the analysis of a 30 residues PVA polymer chain in SPC water.

I'm trying to find the dihedral transition times of each residue (possibly
as an histogram 'number of transitions vs. residue number').
I've already tried:

1) g_angle -f traj.trr -s topol.tpr -n angle.ndx -oh histo.xvg
but it gives no output besides angdist.xvg

2) g_dih -f traj.trr -s topol.tpr -o dihe.out
but it gives no output besides an empty dihe.out

3) g_chi (it says there are no dihedral angles in the structure. I guess
that this program is for proteins only and it doesn't recognize PVA backbone
I've tried these programs on both gromacs 4.5.3 and gromacs 3.3.3.

Thanks for any incoming help!

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