[gmx-users] doing averages using g_angle

[Mark Abraham]

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>> 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>>> 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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