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g_angle - calculates distributions and correlations for angles and dihedralsVERSION4.0.1

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

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-ora trajectory file is dumped containing cos andsin of selected dihedral angles which subsequently can be used as input for a PCA analysis usingg_covar.

-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

-[no]hnoPrint help 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, eps and pdb files-[no]xvgryesAdd specific codes (legends etc.) in the output xvg files for the xmgrace program-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 || 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,exp7orexp9-ncskipint0Skip N 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 till the end

- Counting transitions only works for dihedrals with multiplicity 3

gromacs(7)More information aboutGROMACSis available at <http://www.gromacs.org/>. Thu 16 Oct 2008 g_angle(1)