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g_angleMain Table of Contents |
VERSION 4.5
Thu 26 Aug 2010
| VERSION 4.5 |
g_angle computes the angle distribution for a number of angles or dihedrals. This way you can check whether your simulation is correct. With option -ov you can plot the average angle of a group of angles as a function of time. With the -all option the first graph is the average, the rest are the individual angles.
With the -of option g_angle also calculates the fraction of trans dihedrals (only for dihedrals) as function of time, but this is probably only fun for a selected few.
With option -oc a dihedral correlation function is calculated.
It should be noted that the indexfile should contain atom-triples for angles or atom-quadruplets for dihedrals. If this is not the case, the program will crash.
With option -or a trajectory file is dumped containing cos and sin of selected dihedral angles which subsequently can be used as input for a PCA analysis using g_covar.
| option | filename | type | description |
|---|---|---|---|
| -f | traj.xtc | Input | Trajectory: xtc trr trj gro g96 pdb cpt |
| -n | angle.ndx | Input | Index file |
| -od | angdist.xvg | Output | xvgr/xmgr file |
| -ov | angaver.xvg | Output, Opt. | xvgr/xmgr file |
| -of | dihfrac.xvg | Output, Opt. | xvgr/xmgr file |
| -ot | dihtrans.xvg | Output, Opt. | xvgr/xmgr file |
| -oh | trhisto.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 | default | description |
|---|---|---|---|
| -[no]h | gmx_bool | no | Print help info and quit |
| -[no]version | gmx_bool | no | Print version info and quit |
| -nice | int | 19 | Set the nicelevel |
| -b | time | 0 | 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 | gmx_bool | no | View output xvg, xpm, eps and pdb files |
| -xvg | enum | xmgrace | xvg plot formatting: xmgrace, xmgr or none |
| -type | enum | angle | Type of angle to analyse: angle, dihedral, improper or ryckaert-bellemans |
| -[no]all | gmx_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 | gmx_bool | yes | Print dihedral angles modulo 360 degrees |
| -[no]chandler | gmx_bool | no | Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi < -60 || phi > 60. |
| -[no]avercorr | gmx_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 | gmx_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 or exp9 |
| -ncskip | int | 0 | Skip N 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 |