Provided by: gromacs-data_4.6.5-1build1_all

**NAME**

g_angle - calculates distributions and correlations for angles and dihedralsVERSION4.6.5

**SYNOPSIS**

g_angle-ftraj.xtc-nangle.ndx-odangdist.xvg-ovangaver.xvg-ofdihfrac.xvg-otdihtrans.xvg-ohtrhisto.xvg-ocdihcorr.xvg-ortraj.trr-[no]h-[no]version-niceint-btime-etime-dttime-[no]w-xvgenum-typeenum-[no]all-binwidthreal-[no]periodic-[no]chandler-[no]avercorr-acflenint-[no]normalize-Penum-fitfnenum-ncskipint-beginfitreal-endfitreal

**DESCRIPTION**

g_anglecomputes the angle distribution for a number of angles or dihedrals. With option-ov, you can plot the average angle of a group of angles as a function of time. With the-alloption, the first graph is the average and the rest are the individual angles. With the-ofoption,g_anglealso calculates the fraction of trans dihedrals (only for dihedrals) as function of time, but this is probably only fun for a select few. With option-oc, a dihedral correlation function is calculated. It should be noted that the index file must contain atom triplets 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 principal components analysis usingg_covar. Option-otplots when transitions occur between dihedral rotamers of multiplicity 3 and-ohrecords a histogram of the times between such transitions, assuming the input trajectory frames are equally spaced in time.

**FILES**

-ftraj.xtcInputTrajectory: xtc trr trj gro g96 pdb cpt-nangle.ndxInputIndex file-odangdist.xvgOutputxvgr/xmgr file-ovangaver.xvgOutput,Opt.xvgr/xmgr file-ofdihfrac.xvgOutput,Opt.xvgr/xmgr file-otdihtrans.xvgOutput,Opt.xvgr/xmgr file-ohtrhisto.xvgOutput,Opt.xvgr/xmgr file-ocdihcorr.xvgOutput,Opt.xvgr/xmgr file-ortraj.trrOutput,Opt.Trajectory in portable xdr format

**OTHER** **OPTIONS**

-[no]hnoPrint help info and quit-[no]versionnoPrint version info and quit-niceint19Set the nicelevel-btime0First frame (ps) to read from trajectory-etime0Last frame (ps) to read from trajectory-dttime0Only use frame when t MOD dt = first time (ps)-[no]wnoView output.xvg,.xpm,.epsand.pdbfiles-xvgenumxmgracexvg plot formatting:xmgrace,xmgrornone-typeenumangleType of angle to analyse:angle,dihedral,improperorryckaert-bellemans-[no]allnoPlot all angles separately in the averages file, in the order of appearance in the index file.-binwidthreal1binwidth (degrees) for calculating the distribution-[no]periodicyesPrint dihedral angles modulo 360 degrees-[no]chandlernoUse Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi -60 or phi 60.-[no]avercorrnoAverage the correlation functions for the individual angles/dihedrals-acflenint-1Length of the ACF, default is half the number of frames-[no]normalizeyesNormalize ACF-Penum0Order of Legendre polynomial for ACF (0 indicates none):0,1,2or3-fitfnenumnoneFit function:none,exp,aexp,exp_exp,vac,exp5,exp7,exp9orerffit-ncskipint0Skip this many points in the output file of correlation functions-beginfitreal0Time where to begin the exponential fit of the correlation function-endfitreal-1Time 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 3

**SEE** **ALSO**

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Mon 2 Dec 2013 g_angle(1)