[gmx-users] using g_angle
francesca vitalini
francesca.vitalini11 at gmail.com
Thu Mar 1 10:27:55 CET 2012
Hi all!
I have a question about how g_angle works. Form what I understood from
the manual, if I provide an index file with dihedral quadruplets, then
g_angle with the options -ov -all and -type dihedral should give me a
list of dihedral values one for each quadruplet. However when I do
that I obtain 2 values more than the input number of quadruplets and I
don't understand why. Is it here something I'm missing from how it
works?
Thanks for any help.
Francesca
2012/2/29 francesca vitalini <francesca.vitalini11 at gmail.com>:
> 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
>>>>>> --
>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>> interface
>>>>>> or send it to gmx-users-request at gromacs.org.
>>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>
>>>>
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface
>>>> or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
> 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
More information about the gromacs.org_gmx-users
mailing list