[gmx-users] Re: gmx-users Digest, Vol 83, Issue 41

[sa]

OK, i will try your suggestion.

Thank you

SA

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
> >
> >     ========================================
> >
> >
>
> --
>
>
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