[gmx-users] using g_angle
francesca.vitalini11 at gmail.com
Wed Feb 29 15:00:02 CET 2012
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
[ 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 ""
@ subtitle "average angle: -6192.3\So\N"
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?
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
>> 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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