[gmx-users] using g_angle

[Vedat Durmaz]

hi francesca,

i think what you are looking for is this

g_sgangle $indexFile -f $traj -s $tpr -oa $outfile


before that, you have to define two planes (by 3 atom indices each) in 
your index file

[ dihed1 ]
523 680 3482
[ dihed2 ]
680 3482 3691

which you choose when having started g_sgangle.

the most important part is the -oa option!! what you get then is 
something like

...
#@    title "Angle between dihed1 and dihed2"
#@    xaxis  label "Time (ps)"
#@    yaxis  label "Angle (degrees)"
#@TYPE xy
            0        0.9226       22.6908
          0.4      0.930216       21.5314
          0.8      0.930954       21.4159
          1.2      0.927077       22.0163
          1.6      0.935084       20.7583
            2      0.933544       21.0059
          2.4      0.928635        21.777
          2.8      0.916627       23.5621
          3.2      0.923862       22.5027
...


ciao
vedat



Am 29.02.2012 13:54, schrieb francesca vitalini:
> 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.
>
>>> 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
> ...
> 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?
> Thanks
>
>> Mark
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