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

Cristi Amariei fenix.90 at hotmail.it
Fri Feb 13 16:50:46 CET 2015

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
-[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 >
-[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
-[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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