[gmx-users] using g_angle
francesca vitalini
francesca.vitalini11 at gmail.com
Wed Feb 29 16:24:01 CET 2012
Thank you. It worked now.
Best
Francesca
2012/2/29 Mark Abraham <Mark.Abraham at anu.edu.au>:
> On 1/03/2012 1:00 AM, francesca vitalini wrote:
>>
>> Hi Mark,
>> Thanks for your answer. What I'm trying to do is calculate the value
>> in degrees of the angles listed in my index file. If my index file
>> looks like
>> [ dihedral 1 ]
>> 2 7 9 10
>> [ dihedral 2 ]
>> 10 16 18 19
>
>
> I said in my last email that my suggestion of a separate group group for
> each angle was wrong and that your original index file like
>
>
> [ dihedrals ]
> 2 5 9 10
> 10 15 18 19
> .....
>
> was fine. Please try that with g_angle -ov -all. I get output like
>
> # This file was created Mon Feb 20 12:32:15 2012
>
> # by the following command:
> # g_angle -f 005_5 -type dihedral -all -ov 005_5_angles.xvg -n
> ../1oei_sim_backbone_angle.ndx
> #
> # g_angle is part of G R O M A C S:
> #
> # GRoups of Organic Molecules in ACtion for Science
> #
> @ title "Average Angle: Backbone_dihedral_angles"
> @ xaxis label "Time (ps)"
> @ yaxis label "Angle (degrees)"
> @TYPE xy
> 245757.00000 19.937 1.923 -61.394 -74.236 27.453 -2.719
> -179.194 96.730 -27.468 43.121 -8.608 -0.480 -0.764
> 0.001 -179.750 170.982 157.245 -174.933 37.563 40.854 93.329
> 19.823 169.543 129.371 40.443 -149.558 8.198 43.427
> 100.089 86.565 154.344 171.804 52.401 -158.571 27.166
> -143.253 39.944 6.985 178.488 179.865 -0.432 179.965
> -179.957 179.499 -179.774 -179.788 107.176 151.312 -37.770
> 245762.00000 22.309 -1.821 -60.416 -73.830 -21.904 -2.231
> -179.111 96.693 -114.414 40.600 -154.543 0.922 -2.143
> 0.932 179.704 -71.467 147.204 171.571 52.328 39.069 70.499
> 3.113 179.355 91.086 43.155 133.656 -22.505 23.643
> 104.997 105.160 151.335 -176.456 176.378 23.691 6.447 -102.512
> 43.837 33.328 -179.572 -179.286 1.288 179.801 179.207
> -179.029 -178.575 179.950 151.692 164.967 -4.967
> 245763.00000 36.760 -1.567 -59.734 -74.259 -88.956 9.191
> 175.880 91.328 -106.962 38.466 -159.767 -0.092 1.363
> -0.665 -179.743 -63.435 159.398 168.167 42.926 40.201
> 86.058 15.792 171.260 108.564 37.481 148.734 -19.163
> 41.603 95.716 100.927 159.081 177.076 170.625 18.814
> 11.879 -108.608 42.251 31.301 -179.193 -179.047 0.401
> -179.484 179.431 179.957 179.578 179.770 143.532 159.744
> -1.341
>
>
> Mark
>
>
>> then if I use the command line
>>
>> g_angle -f aa.gro -s aa.tpr -n angles_prova.ndx -ov angav_prova3.xvg
>> -all -type dihedral
>> or the same with the flag -od,
>> what I get is an interactive menu where I have to choose the group and
>> if I choose one then I obtain an output file which looks like
>> # This file was created Wed Feb 29 14:54:55 2012
>> # by the following command:
>> # /home/cocktail/vitalini/gromacs_special/bin/g_angle -f aa.gro -s
>> aa.tpr -n angles_prova.ndx -od angav_prova3.xvg -all -type dihedral
>> #
>> # /home/cocktail/vitalini/gromacs_special/bin/g_angle is part of G R O M A
>> C S:
>> #
>> # Great Red Oystrich Makes All Chemists Sane
>> #
>> @ title "Dihedral Distribution: dihedral"
>> @ xaxis label "Degrees"
>> @ yaxis label ""
>> @TYPE xy
>> @ subtitle "average angle: -6192.3\So\N"
>> -109 0.000000
>> -108 1.000000
>> -107 0.000000
>>
>> Which does what I'm looking for but this means that I'll need a file
>> for each angle. Is there a faster way to get a file that has like two
>> columns, one for the dihedral and another one for the angles?
>> Thanks
>> Francesca
>>
>> 2012/2/29 Mark Abraham<Mark.Abraham at anu.edu.au>:
>>>
>>> On 29/02/2012 11:54 PM, francesca vitalini wrote:
>>>>
>>>> 2012/2/29 Mark Abraham<Mark.Abraham at anu.edu.au>:
>>>>>
>>>>> On 29/02/2012 9:39 PM, francesca vitalini wrote:
>>>>>>
>>>>>> Hi all,
>>>>>> I'm trying to use g_angle to calculate a list of dihedrals that I have
>>>>>> into an hand made index file (angles.ndx), which looks like
>>>>>> [ dihedrals ]
>>>>>> 2 5 9 10
>>>>>> 10 15 18 19
>>>>>> .....
>>>>>
>>>>>
>>>>> mk_angndx might have helped.
>>>>
>>>> Actually mk_angndx gies me the angles for phi and psi while instead I
>>>> need omega and they are put in a strange format like in groups of 8
>>>> instead of 4.
>>>
>>>
>>> Whitespace inside the index group probably doesn't matter.
>>>
>>>
>>>>>> However it produces a .xvg file where it gives me for each angle in
>>>>>> degrees its probability. However, what I want is instead to know the
>>>>>> value in degrees of each angle in the ndx file. Do you have any
>>>>>> suggestions apart from building an index file for each angle?
>>>>>
>>>>>
>>>>> g_angle -ov -all with each angle in its own group.
>>>>
>>>> What do you mean with each angle in its own group? something like
>>>> [dihedrals]
>>>> 2 5 9 10
>>>> [dihedrals]
>>>> 10 13 16 18
>>>> ...
>>>
>>>
>>> Yes, but with unique group names - but it turns out I was wrong to
>>> suggest
>>> that. Your index file above is fine.
>>>
>>>
>>>> Isn't it equivalent to build differend index files?
>>>> anyway the -ov flag gives the average over time, but I need the angles
>>>> just at one time, that is why I was using -od but it just plots the
>>>> distribution of all angles together.
>>>> Any help?
>>>
>>>
>>> Which part of the output of g_angle -ov **-all** doesn't suit you?
>>>
>>> Mark
>>>
>>>
>>>> Thanks
>>>>
>>>>> Mark
>>>>> --
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>>>>
>>>>
>>>>
>>>> --
>>>
>>>
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>
>
> --
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--
Francesca Vitalini
PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin
vitalini at zedat.fu-berlin.de
francesca.vitalini at fu-berlin.de
+49 3083875776
+49 3083875412
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