Hi all! I have a question about how g_angle works. Form what I understood from the manual, if I provide an index file with dihedral quadruplets, then g_angle with the options -ov -all and -type dihedral should give me a list of dihedral values one for each quadruplet. However when I do that I obtain 2 values more than the input number of quadruplets and I don't understand why. Is it here something I'm missing from how it works? Thanks for any help. Francesca
2012/2/29 francesca vitalini <francesca.vitalin...@gmail.com>: > Thank you. It worked now. > Best > Francesca > > > > 2012/2/29 Mark Abraham <mark.abra...@anu.edu.au>: >> 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 >>>>>> -- >>>>>> gmx-users mailing list gmx-users@gromacs.org >>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>>>> Please search the archive at >>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>>>> Please don't post (un)subscribe requests to the list. Use the www >>>>>> interface >>>>>> or send it to gmx-users-requ...@gromacs.org. >>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> >>>>> >>>>> -- >>>> >>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> Please don't post (un)subscribe requests to the list. Use the www >>>> interface >>>> or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www interface >> or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > Francesca Vitalini > > PhD student at Computational Molecular Biology Group, > Department of Mathematics and Informatics, FU-Berlin > Arnimallee 6 14195 Berlin > > vital...@zedat.fu-berlin.de > francesca.vital...@fu-berlin.de > > +49 3083875776 > +49 3083875412 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
