[gmx-users] doing averages using g_angle
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 ...
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
> 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?
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