[gmx-users] doing averages using g_angle

Amit Choubey kgp.amit at gmail.com
Wed Dec 2 05:07:22 CET 2009

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.

Thank you,

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