[gmx-users] using g_angle

francesca vitalini francesca.vitalini11 at gmail.com
Wed Feb 29 13:54:40 CET 2012

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?

> Mark
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