Hi, As far as I can see, that should work... Looks like a bug, but I can't see why. If you can reproduce it with a small piece of your trajectory, please make a tarball of the input files and file an issue at http://redmine.gromacs.org and I'll take a look.
Thanks, Mark On Feb 13, 2015 4:51 PM, "Cristi Amariei" <fenix...@hotmail.it> wrote: > > > > > > Here is the line command end the output : (by the way the GROMACS's > vertion is 4.6.5 ) > > > > g_angle -type dihedral -f 30iso_amber94_323_2-3_pol.xtc -b 70000 -od prova > -ot t-ptova -oh h-prova -n indicediedri.ndx > ..... > Option Filename Type Description > ------------------------------------------------------------ > -f 30iso_amber94_323_2-3_pol.xtc Input Trajectory: xtc trr trj > gro > g96 pdb cpt > -n indicediedri.ndx Input Index file > -od prova.xvg Output xvgr/xmgr file > -ov angaver.xvg Output, Opt. xvgr/xmgr file > -of dihfrac.xvg Output, Opt. xvgr/xmgr file > -ot t-ptova.xvg Output, Opt! xvgr/xmgr file > -oh h-prova.xvg Output, Opt! xvgr/xmgr file > -oc dihcorr.xvg Output, Opt. xvgr/xmgr file > -or traj.trr Output, Opt. Trajectory in portable xdr format > > Option Type Value Description > ------------------------------------------------------ > -[no]h bool no Print help info and quit > -[no]version bool no Print version info and quit > -nice int 19 Set the nicelevel > -b time 70000 First frame (ps) to read from trajectory > -e time 0 Last frame (ps) to read from trajectory > -dt time 0 Only use frame when t MOD dt = first time (ps) > -[no]w bool no View output .xvg, .xpm, .eps and .pdb files > -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none > -type enum dihedral Type of angle to analyse: angle, dihedral, > improper or ryckaert-bellemans > -[no]all bool no Plot all angles separately in the averages > file, > in the order of appearance in the index file. > -binwidth real 1 binwidth (degrees) for calculating the > distribution > -[no]periodic bool yes Print dihedral angles modulo 360 degrees > -[no]chandler bool no Use Chandler correlation function (N[trans] = > 1, > N[gauche] = 0) rather than cosine correlation > function. Trans is defined as phi < -60 or phi > > > 60. > -[no]avercorr bool no Average the correlation functions for the > individual angles/dihedrals > -acflen int -1 Length of the ACF, default is half the number > of > frames > -[no]normalize bool yes Normalize ACF > -P enum 0 Order of Legendre polynomial for ACF (0 > indicates > none): 0, 1, 2 or 3 > -fitfn enum none Fit function: none, exp, aexp, exp_exp, vac, > exp5, exp7, exp9 or erffit > -ncskip int 0 Skip this many points in the output file of > correlation functions > -beginfit real 0 Time where to begin the exponential fit of the > correlation function > -endfit real -1 Time where to end the exponential fit of the > correlation function, -1 is until the end > > Group 0 ( -CBCACB+CA) has 116 elements > Group 1 ( CACB+CA+CB) has 116 elements > Group 2 ( -CBCACB+CA-) has 232 elements > Group 3 ( diedro) has 4 elements > Group 4 ( diedro2) has 4 elements > Select a group: 3 > Selected 3: 'diedro' > Last frame 10000 time 120000.000 > Found points in the range from 0 to 359 (max 360) > < angle > = -73.7241 > < angle^2 > = 29402 > Std. Dev. = 154.812 > Order parameter S^2 = 0.973661 > > The number of frames is 100000. thanks > > Cristi Amariei > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.