g_rotacf(1) [debian man page]
g_rotacf(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_rotacf(1) NAME
g_rotacf - calculates the rotational correlation function for molecules VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_rotacf -f traj.xtc -s topol.tpr -n index.ndx -o rotacf.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]d -[no]aver -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real DESCRIPTION
g_rotacf calculates the rotational correlation function for molecules. Three atoms (i,j,k) must be given in the index file, defining two vectors ij and jk. The rotational ACF is calculated as the autocorrelation function of the vector n = ij x jk, i.e. the cross product of the two vectors. Since three atoms span a plane, the order of the three atoms does not matter. Optionally, controlled by the -d switch, you can calculate the rotational correlation function for linear molecules by specifying two atoms (i,j) in the index file. EXAMPLES g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1 -beginfit 2.5 -endfit 20.0 This will calculate the rotational correlation function using a first order Legendre polynomial of the angle of a vector defined by the index file. The correlation function will be fitted from 2.5 ps until 20.0 ps to a two-parameter exponential. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input Run input file: tpr tpb tpa -n index.ndx Input Index file -o rotacf.xvg Output xvgr/xmgr file 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 -[no]dno Use index doublets (vectors) for correlation function instead of triplets (planes) -[no]averyes Average over molecules -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 SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_rotacf(1)
Check Out this Related 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-bc5695c SYNOPSIS
g_angle -f traj.xtc -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 -[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 proba- bly 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 3 SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_angle(1)