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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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