[gmx-users] counting dihedral transitions not working with gmx angle (Mark Abraham)

[Mark Abraham]

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.90 at 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
>
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