[gmx-users] doing averages using g_angle
Justin A. Lemkul
jalemkul at vt.edu
Wed Dec 2 21:07:49 CET 2009
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...
-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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