[gmx-users] The dihedral angles from 192 elements ??
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Jul 3 07:10:39 CEST 2008
Lin,
This is manual stuff...:
http://www.gromacs.org/documentation/reference/online/g_angle.html
So the first lines answer your question:
g_angle computes the angle distribution for a number of angles or
dihedrals. This way you can check whether your simulation is correct.
With option -ov you can plot the average angle of a group of angles as
a function of time.
Which clearly (!) states that your first plot is a distribution of all
angles measured over time for each dihedral in your set (piled
together) and that your second plot calculates an average for your set
of dihedrals for each frame.
Tsjerk
On Thu, Jul 3, 2008 at 1:02 AM, Chih-Ying Lin <chihying2008 at gmail.com> wrote:
> Hi
> Four atoms form a set of diheral angles.
>
> When I do g_angle for the dihedral angle calculation, it shows
>
> Group 0 (Phi=180.0_2_70) has 4 elements
> Group 1 (Phi=180.0_2_6) has 16 elements
> Group 2 (Phi=180.0_2_40) has 192 elements
> Select a group:
>
> If I select Group 2, there is 192 elements (192=48*4), it means there
> are 48 sets of dihedal angles).
>
> the command
> g_angle -od angdist.xvg -ov angaver.xvg type diheral
>
> output 2 plots: angdist.xvg and angaver.xvg
>
> what does the two plots mean for the 48 sets of dihedral angles??
> Are the two plots average over the 48 sets of dihedral angles?
>
>
>
> Thanks a lot
> Lin
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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