[gmx-users] using g_angle

[Mark Abraham]

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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