[gmx-users] Using -all flag in g_angle command

[Mark Abraham]

Hi,

Did you look at the full contents of the output files? I expect they're in
the same file produced without -all.

Mark

On Thu, Jan 15, 2015 at 12:47 PM, GAYATHRI S <gayathri.s at iitb.ac.in> wrote:

> The following command generated only two outputs - angaver.xvg and
> angdist.xvg:
>
> $ g_angle -f full.xtc -n dangle.ndx -ov -all -type dihedral
>
> The -all flag is supposed to generate graphs for individual angles, but it
> didn't.
>
>
>
>
> gmx angle -h suggests -ov -all generates multiple graphs, only the first
> > of
> > which is the average. What's in the rest of your output file?
> >
> > Mark
> >
> > On Wed, Jan 14, 2015 at 7:21 AM, GAYATHRI S <gayathri.s at iitb.ac.in>
> wrote:
> >
> >> Hello everyone,
> >>
> >> I simulated an NADH molecule. I want to check how each of the dihedral
> >> angles changes during the simulation. In other words, I want to plot a
> >> graph of individual (not average) dihedral angles versus time.
> >>
> >> To do so, I created an index file using the following command:
> >>
> >> $ mk_angndx -s full.tpr -n angle.ndx -type dihedral
> >>
> >> Next, I used the g_angle command as follows:
> >>
> >> $ g_angle -f full.xtc -n angle.ndx -type dihedral -all
> >>
> >> However, this command generated only one output file angdist.xvg. The
> >> -ov
> >> flag generates angles in degrees; but, it gives values in average and I
> >> want the same plot for individual angles.
> >>
> >> Please suggest how to proceed.
> >>
> >> Thank you.
> >>
> >> --
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