# g_angle(1) [debian man page]

g_angle(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_angle(1)NAME

g_angle - calculates distributions and correlations for angles and dihedrals VERSION 4.5.4-dev-20110404-bc5695cSYNOPSIS

g_angletraj.xtc-fangle.ndx-nangdist.xvg-odangaver.xvg-ovdihfrac.xvg-ofdihtrans.xvg-ottrhisto.xvg-ohdihcorr.xvg-octraj.trr -[no]h -[no]version-orint-nicetime-btime-etime -[no]w-dtenum-xvgenum -[no]all-typereal -[no]periodic -[no]chandler -[no]avercorr-binwidthint -[no]normalize-acflenenum-Penum-fitfnint-ncskipreal-beginfitreal-endfitDESCRIPTION

g_angle computes the angle distribution for a number of angles or dihedrals. This way you can check whether your simulation is correct. With optionyou can plot the average angle of a group of angles as a function of time. With the-ovoption the first graph is the average, the rest are the individual angles. With the-alloption, g_angle also calculates the fraction of trans dihedrals (only for dihedrals) as function of time, but this is proba- bly only fun for a selected few. With option-ofa 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-oca 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.-orFILES

traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt-fangle.ndx Input Index file-nangdist.xvg Output xvgr/xmgr file-odangaver.xvg Output, Opt. xvgr/xmgr file-ovdihfrac.xvg Output, Opt. xvgr/xmgr file-ofdihtrans.xvg Output, Opt. xvgr/xmgr file-ottrhisto.xvg Output, Opt. xvgr/xmgr file-ohdihcorr.xvg Output, Opt. xvgr/xmgr file-octraj.trr Output, Opt. Trajectory in portable xdr format-orOTHER OPTIONS

-[no]hno Print help info and quit -[no]versionno Print version info and quitint 19 Set the nicelevel-nicetime 0 First frame (ps) to read from trajectory-btime 0 Last frame (ps) to read from trajectory-etime 0 Only use frame when t MOD dt = first time (ps) -[no]wno View output .xvg, .xpm, .eps and .pdb files-dtenum xmgrace xvg plot formatting: xmgrace, xmgr or none-xvgenum 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.-typereal 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-binwidthor phi 60. -[no]avercorrno Average the correlation functions for the individual angles/dihedrals-60int-acflenLength of the ACF, default is half the number of frames -[no]normalizeyes Normalize ACF-1enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3-Penum none Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit-fitfnint 0 Skip N points in the output file of correlation functions-ncskipreal 0 Time where to begin the exponential fit of the correlation function-beginfitreal-endfitTime where to end the exponential fit of the correlation function,-1is until the end-1KNOWN PROBLEMS

- Counting transitions only works for dihedrals with multiplicity 3SEE ALSO

gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_angle(1)