[gmx-users] Re: gmx-users Digest, Vol 83, Issue 40

[sa]

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

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