[gmx-users] Dihedral angles distribution

[Justin A. Lemkul]

sa wrote:
> Dear GMXusers
> 
> I would like to obtain the normalized CCCC dihedral distribution of the 
> alkyl chain of DPC molecules simulated with the CHARMM ff and GMX4.5.3. 
> So i used the g_angle tool. I have constructed an index file which 
> contain the 9 corresponding angles with make_index_mpi:
> 
> a C12 | a C13 | a C14 | a C15 ---> consecutive atoms
> ...
> a C20 | a C21 | a C22 | aC23
> 
> and used g_angle command
> 
> g_angle_mpi -f *.xtc -ov DPC-Self-CHA_100-155ns-Angle_0_Dihed.xvg -b 
> 100000 -e 110000 -n Tail_dihedral_index.ndx -type dihedral
> 
> For example by choosing the C15_C16_C17_C18 dihedral angle located in 
> the middle of the alkyl chain, i obtain an average value 0° (!!) and the 
> following figure
> 
> http://www.hostingpics.net/viewer.php?id=825755angdist.png
> 
> This  is not what i expect How to obtain simply the classical normalized 
> function from g_angle ?

You're taking an average of the histogram of the angles, which I don't think 
actually corresponds to the true average.  Your biggest peaks are at +/- 180 
(i.e., trans dihedral), so I suspect your mean is likely not really 0.  Use 
g_angle -ov to get an actual average over time.

-Justin

> 
> Thank you in advance for your advices
> 
> SA
> 
> 
> 

-- 
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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

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