g_angle VERSION 3.3_beta_20050823

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 -or traj.trr -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -type enum -[no]all -binwidth real -[no]chandler -[no]avercorr -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real

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

-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

-or traj.trr Output, Opt. Trajectory in portable xdr format

-[no]h no 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]w no View output xvg, xpm, eps and pdb files

-[no]xvgr yes 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]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

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.