[gmx-users] doing averages using g_angle
Amit Choubey
kgp.amit at gmail.com
Wed Dec 2 21:17:05 CET 2009
On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Amit Choubey wrote:
>
>> Hi Mark,
>>
>> That is true. But what does the manual refer to when it says
>> the first graph is the average, the rest are the individual angles
>>
>> what and where are the rest? I am only curious because there might be a
>> hidden feature that could be useful for me.
>>
>>
> Read all of the help information; the command in the .xvg file below shows
> that you're not yet using the right output options. Hint: look at the
> sentence in g_angle -h before the one quoted above, as well as the -ov
> flag...
>
-ov flag gives the average value of angle of the group with time. This is
not very useful for me right now.
I am interested in the distribution of dihedrals with angle.
I was just curious about the -all features...
>
> -Justin
>
> Amit
>>
>>
>> On Wed, Dec 2, 2009 at 12:21 AM, Mark Abraham <Mark.Abraham at anu.edu.au<mailto:
>> Mark.Abraham at anu.edu.au>> wrote:
>>
>> 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>
>> <mailto: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>>
>> <mailto: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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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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