[gmx-users] Dihedral angles distribution

[Justin A. Lemkul]

sa wrote:
> Yes justin, the average is not 0 but around 0° (0.584577). But how to 
> obtain the Average normalized CCCC dihedral distribution for example 
> this dihedral?  is few words the figure with g_angle ?
> 
> http://cmt.dur.ac.uk/sjc/thesis_dlc/node106.html
> 

The output you will get from Gromacs will have all angles within the range of 
{-180..180}, not {0..360}, as shown in that plot.  I think this simply derives 
from a difference in convention.  You would have to post-process the data to 
shift the angles to correspond to the display range you want.  Gromacs does not 
do this for you.  To get the "correct" average angle, use g_angle -noperiodic.

-Justin

> Thank you again
> 
>  
> 
>     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
>      >
>      >
>      >
> 
>     --
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
> 
> 

-- 
========================================

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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