g_angle(1) - Linux man page

Name

g_angle - calculates distributions and correlations for angles and dihedrals

VERSION 4.5.4-dev-20110404-bc5695c

Synopsis

g_angle -f traj.xtc -n angle.ndx -odangdist.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 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 index file 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.

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

-[no]versionno 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]wno 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]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 or 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, exp9 or erffit

-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

- Counting transitions only works for dihedrals with multiplicity