| 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 |