On 1/03/2012 1:00 AM, francesca vitalini wrote:
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
I said in my last email that my suggestion of a separate group group for
each angle was wrong and that your original index file like
[ dihedrals ]
2 5 9 10
10 15 18 19
.....
was fine. Please try that with g_angle -ov -all. I get output like
# This file was created Mon Feb 20 12:32:15 2012
# by the following command:
# g_angle -f 005_5 -type dihedral -all -ov 005_5_angles.xvg -n
../1oei_sim_backbone_angle.ndx
#
# g_angle is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@ title "Average Angle: Backbone_dihedral_angles"
@ xaxis label "Time (ps)"
@ yaxis label "Angle (degrees)"
@TYPE xy
245757.00000 19.937 1.923 -61.394 -74.236 27.453
-2.719 -179.194 96.730 -27.468 43.121 -8.608 -0.480
-0.764 0.001 -179.750 170.982 157.245 -174.933 37.563
40.854 93.329 19.823 169.543 129.371 40.443 -149.558
8.198 43.427 100.089 86.565 154.344 171.804 52.401
-158.571 27.166 -143.253 39.944 6.985 178.488 179.865
-0.432 179.965 -179.957 179.499 -179.774 -179.788 107.176
151.312 -37.770
245762.00000 22.309 -1.821 -60.416 -73.830 -21.904
-2.231 -179.111 96.693 -114.414 40.600 -154.543 0.922
-2.143 0.932 179.704 -71.467 147.204 171.571 52.328
39.069 70.499 3.113 179.355 91.086 43.155 133.656
-22.505 23.643 104.997 105.160 151.335 -176.456 176.378
23.691 6.447 -102.512 43.837 33.328 -179.572 -179.286
1.288 179.801 179.207 -179.029 -178.575 179.950 151.692
164.967 -4.967
245763.00000 36.760 -1.567 -59.734 -74.259 -88.956
9.191 175.880 91.328 -106.962 38.466 -159.767 -0.092
1.363 -0.665 -179.743 -63.435 159.398 168.167 42.926
40.201 86.058 15.792 171.260 108.564 37.481 148.734
-19.163 41.603 95.716 100.927 159.081 177.076 170.625
18.814 11.879 -108.608 42.251 31.301 -179.193 -179.047
0.401 -179.484 179.431 179.957 179.578 179.770 143.532
159.744 -1.341
Mark
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.abra...@anu.edu.au>:
On 29/02/2012 11:54 PM, francesca vitalini wrote:
2012/2/29 Mark Abraham<mark.abra...@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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