[gmx-users] doing averages using g_angle

Amit Choubey kgp.amit at gmail.com
Wed Dec 2 21:17:05 CET 2009


On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Amit Choubey wrote:
>
>> Hi Mark,
>>
>> That is true. But what does the manual refer to when it says
>> the first graph is the average, the rest are the individual angles
>>
>> what and where are the rest? I am only curious because there might be a
>> hidden feature that could be useful for me.
>>
>>
> Read all of the help information; the command in the .xvg file below shows
> that you're not yet using the right output options.  Hint: look at the
> sentence in g_angle -h before the one quoted above, as well as the -ov
> flag...
>

-ov flag gives the average value of angle of the group with time. This is
not very useful for me right now.

I am interested in the distribution of dihedrals with angle.

I was just curious about the -all features...



>
> -Justin
>
>  Amit
>>
>>
>> On Wed, Dec 2, 2009 at 12:21 AM, Mark Abraham <Mark.Abraham at anu.edu.au<mailto:
>> Mark.Abraham at anu.edu.au>> wrote:
>>
>>    Amit Choubey wrote:
>>
>>        Hi Mark,
>>
>>        Ok here is the command line i used :-
>>
>>        g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e
>>        804 -all
>>        output is
>>        # This file was created Tue Dec  1 20:20:41 2009
>>        # by the following command:
>>        # g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e
>>        804 -all
>>        #
>>        # g_angle is part of G R O M A C S:
>>        #
>>        # Go Rough, Oppose Many Angry Chinese Serial killers
>>        #
>>        @    title "Dihedral Distribution: C34_C36_C37_C38"
>>
>>
>>    This title makes it look like there is only one angle in your index
>>    file.
>>
>>    Mark
>>
>>        @    xaxis  label "Degrees"
>>        @    yaxis  label ""
>>        @TYPE xy
>>        @    subtitle "average angle: 9.87432\So\N"
>>        @with g0
>>        @    world xmin -180
>>        @    world xmax  180
>>        @    world ymin 0
>>        @    world ymax 0.0451172
>>        @    xaxis  tick major 60
>>        @    xaxis  tick minor 30
>>        @    yaxis  tick major 0.005
>>        @    yaxis  tick minor 0.0025
>>             -180    0.015625
>>             -179    0.011719
>>             -178    0.015625
>>             -177    0.000000
>>             -176    0.035156
>>             -175    0.031250
>>             -174    0.019531
>>             -173    0.019531
>>             -172    0.023438
>>             -171    0.015625
>>             -170    0.015625
>>
>>        I did not include the distribution for rest of the angles.
>>         The second column is the fractional distribution of dihedrals
>>        with the corresponding angle in the 1st column.
>>
>>        The distribution is averaged over time t = 800ps and 802 ps
>>        snapshots. I checked this part.
>>
>>        Amit
>>
>>
>>
>>
>>        On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham
>>        <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
>>        <mailto:Mark.Abraham at anu.edu.au
>>        <mailto:Mark.Abraham at anu.edu.au>>> wrote:
>>
>>           Amit Choubey wrote:
>>
>>               Hi Mark,
>>
>>               It does seem that the -all option averages the
>> distributions.
>>               The thing is i was confused with "the first graph is the
>>               average, the rest are the individual angles." because when i
>>               tried it previously i only found 2 columns which were
>>        angle and
>>               distribution.
>>
>>               But now i checked again explicitly by doing few more g_angle
>>               commands and it seems that -all does do what i wanted to
>>        do. I
>>               still dont know what the "rest are the individual angles"
>>        means.
>>
>>
>>           I haven't ever used it, but would have expected the output to be
>>           along the lines of
>>
>>           Time "Average over all angles" Angle-1 Angle-2 ...
>>           1          234                   23      345
>>           2          123                   234     232
>>           2          223                   ...
>>           3          323
>>
>>           What output do you get and what seems wrong to you?
>>
>>           Mark
>>
>>               On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham
>>               <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
>>        <mailto:Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>>
>>               <mailto:Mark.Abraham at anu.edu.au
>>        <mailto:Mark.Abraham at anu.edu.au>
>>               <mailto:Mark.Abraham at anu.edu.au
>>        <mailto:Mark.Abraham at anu.edu.au>>>> wrote:
>>
>>                  Amit Choubey wrote:
>>
>>                      Hi everyone,
>>
>>                      I am trying to analyze dihedrals of molecules after a
>>                      simulation. I am able to calculate dihedral
>>        distribution
>>               at ant
>>                      particular time using g
>>                      -angle and proper group using
>>
>>                      g_angle -f after_md.trr -b 800 -type dihedral -n
>>               chain1.ndx -od
>>                      dihed12
>>
>>                      This gives me the distribution at t=800 ps . What i
>>               really want
>>                      is to see the dihedral distribution at all time steps
>>               (after 800
>>                      ps) in one go, and may be do some averaging later.
>>        Is there a
>>                      straight forward way to do this. I can imagine
>>        that i could
>>                      write a script file that could do this but then i
>> dont
>>               want to
>>                      deal with a lot of files, i rather want everything
>>        to be
>>               saved
>>                      in a single file with multiple columns. Could someone
>>               suggest a
>>                      trick for this?
>>
>>
>>                  The first paragraph of g_angle -h suggests there's an
>>        option
>>               where
>>                  "the first graph is the average, the rest are the
>>        individual
>>                  angles." Does this work?
>>
>>
>>                  Mark
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> --
> ========================================
>
> 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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