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

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 4 15:53:50 CEST 2011

Giulio Tesei wrote:
> Hi!
> 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

Add "-type dihedral" to this command, otherwise the analysis is for normal angles.


> 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 dihedrals...).
> I've tried these programs on both gromacs 4.5.3 and gromacs 3.3.3.
> Thanks for any incoming help!
> Giulio


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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