table of contents
g_angle(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_angle(1) |
NAME¶
g_angle - calculates distributions and correlations for angles and dihedralsSYNOPSIS¶
g_angle -f traj.xtc -n angle.ndx -od angdist.xvg -ov angaver.xvg -of dihfrac.xvg -ot dihtrans.xvg -oh trhisto.xvg -oc dihcorr.xvg -or traj.trr -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -type enum -[no]all -binwidth real -[no]periodic -[no]chandler -[no]avercorr -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit realDESCRIPTION¶
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.FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Index file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
xvgr/xmgr file
Trajectory in portable xdr format
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Type of angle to analyse: angle, dihedral, improper or ryckaert-bellemans
Plot all angles separately in the averages file, in the order of appearance in the index file.
binwidth (degrees) for calculating the distribution
Print dihedral angles modulo 360 degrees
Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi -60 or phi 60.
Average the correlation functions for the individual angles/dihedrals
Length of the ACF, default is half the number of frames
Normalize ACF
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit
Skip N points in the output file of correlation functions
Time where to begin the exponential fit of the correlation function
Time where to end the exponential fit of the correlation function, -1 is until the end
KNOWN PROBLEMS¶
- Counting transitions only works for dihedrals with multiplicity 3SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |