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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