Main Table of Contents

Thu 26 Aug 2010


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.


-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

Other options

-[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

Known problems