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

[GAYATHRI S]

Got it! Thank you.


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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>>
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