[gmx-users] doing averages using g_angle
Amit Choubey
kgp.amit at gmail.com
Wed Dec 2 20:56:24 CET 2009
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.
Amit
On Wed, Dec 2, 2009 at 12:21 AM, Mark Abraham <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>> 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>>> 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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