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

[Giulio Tesei]

I'm sorry, actually I forgot to add the flag in the email but I added it
when I started the program.

g_angle -f traj.trr -s topol.tpr -n dihe.ndx -oh histo.xvg -type dihedral
I get the following output:

Group     0 (Phi=0.0_3_5.92) has   232 elements
There is one group in the index
Reading file diheA3.tpr, VERSION 3.3.3 (single precision)
trn version: GMX_trn_file (single precision)
Last frame      10000 time 20000.000
Found points in the range from 0 to 359 (max 360)
 < angle >  = 0.374572
< angle^2 > = 262.338
Std. Dev.   = 16.1925
Order parameter S^2 = 0.344698

but it generates only a angdist.xvg file.
I'm wondering why it's not generating the histo.xvg file.
Thanks for your help!

2011/10/4 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> 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.
>
> -Justin
>
>
>  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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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