[gmx-users] using g_angle
Mark.Abraham at anu.edu.au
Wed Feb 29 14:44:00 CET 2012
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
> 2 5 9 10
> 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?
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