g_angle(1)

NAME
g_angle VERSION 3.2.0

SYNOPSIS
g_angle -f traj.xtc -s topol.tpr -n angle.ndx -od angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oh trhisto.xvg -oc dihcorr.xvg -[no]h -nice int -b time -e time -dt time -[no]w -type enum -[no]all -binwidth real -[no]chandler -[no]avercorr -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real

DESCRIPTION
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.

FILES
-f traj.xtc Input
 Generic trajectory: xtc trr trj gro g96 pdb -s topol.tpr Input
 Generic run input: tpr tpb tpa xml -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

OTHER OPTIONS
-[no]h no
 Print help info and quit -nice int 19
 Set the nicelevel -b time -1
 First frame (ps) to read from trajectory -e time -1
 Last frame (ps) to read from trajectory -dt time -1
 Only use frame when t MOD dt = first time (ps) -[no]w no
 View output xvg, xpm, eps and pdb files -type enum angle
 Type of angle to analyse: angle , dihedral , improper or ryckaert-bellemans -[no]all 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]chandler 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 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 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 till the end - Counting transitions only works for dihedrals with multiplicity 3