[gmx-users] doing averages using g_angle

[Amit Choubey]

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"
@    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>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>> 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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