[gmx-users] using g_angle
durmaz at zib.de
Wed Feb 29 14:12:45 CET 2012
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
#@ title "Angle between dihed1 and dihed2"
#@ xaxis label "Time (ps)"
#@ yaxis label "Angle (degrees)"
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
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
> 2 5 9 10
> 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?
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