[gmx-users] doing averages using g_angle

Mark Abraham Mark.Abraham at anu.edu.au
Wed Dec 2 05:15:56 CET 2009

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?


> On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham <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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