[gmx-users] using g_angle
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Feb 29 16:00:55 CET 2012
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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