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.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