[gmx-users] using g_angle

[francesca vitalini]

Hi Mark,
Thanks for your answer. What I'm trying to do is calculate the value
in degrees of  the angles listed in my index file. If my index file
looks like
[ dihedral 1 ]
2  7  9  10
[ dihedral 2 ]
10  16  18  19
then if I use the command line

g_angle -f aa.gro -s aa.tpr -n angles_prova.ndx -ov angav_prova3.xvg
-all -type dihedral
or the same with the flag -od,
what I get is an interactive menu where I have to choose the group and
if I choose one then I obtain an output file which looks like
# This file was created Wed Feb 29 14:54:55 2012
# by the following command:
# /home/cocktail/vitalini/gromacs_special/bin/g_angle -f aa.gro -s
aa.tpr -n angles_prova.ndx -od angav_prova3.xvg -all -type dihedral
#
# /home/cocktail/vitalini/gromacs_special/bin/g_angle is part of G R O M A C S:
#
# Great Red Oystrich Makes All Chemists Sane
#
@    title "Dihedral Distribution: dihedral"
@    xaxis  label "Degrees"
@    yaxis  label ""
@TYPE xy
@    subtitle "average angle: -6192.3\So\N"
      -109    0.000000
      -108    1.000000
      -107    0.000000

Which does what I'm looking for but this means that I'll need a file
for each angle. Is there a faster way to get a file that has like two
columns, one for the dihedral and another one for the angles?
Thanks
Francesca

2012/2/29 Mark Abraham <Mark.Abraham at anu.edu.au>:
> 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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>>
>>
>> --
>
>
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