g_angle_d (1) - Linux Man Pages

g_angle_d: calculates distributions and correlations for angles and dihedrals

NAME

g_angle - calculates distributions and correlations for angles and dihedrals

VERSION 4.0.1

SYNOPSIS

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 -nice int -b time -e time -dt time -[no]w -[no]xvgr -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 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.

With option -or a trajectory file is dumped containing cos andsin of selected dihedral angles which subsequently can be used as input for a PCA analysis using g_covar.

FILES

-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]hno
 Print help 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]wno
 View output xvg, xpm, eps and pdb files

-[no]xvgryes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-type enum angle
 Type of angle to analyse:  angle dihedral improper or  ryckaert-bellemans

-[no]allno
 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]periodicyes
 Print dihedral angles modulo 360 degrees

-[no]chandlerno
 Use Chandler correlation function (N[trans] 1, N[gauche] 0) rather than cosine correlation function. Trans is defined as phi  -60 || phi  60.

-[no]avercorrno
 Average the correlation functions for the individual angles/dihedrals

-acflen int -1
 Length of the ACF, default is half the number of frames

-[no]normalizeyes
 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

KNOWN PROBLEMS

- Counting transitions only works for dihedrals with multiplicity 3

SEE ALSO

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.