1 .TH g_rotacf 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
3 g_rotacf - calculates the rotational correlation function for molecules
5 .B VERSION 4.5.4-dev-20110404-bc5695c
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
11 .BI "\-o" " rotacf.xvg "
13 .BI "\-[no]version" ""
22 .BI "\-acflen" " int "
23 .BI "\-[no]normalize" ""
25 .BI "\-fitfn" " enum "
26 .BI "\-ncskip" " int "
27 .BI "\-beginfit" " real "
28 .BI "\-endfit" " real "
30 \&\fB g_rotacf\fR calculates the rotational correlation function
31 \&for molecules. Three atoms (i,j,k) must be given in the index
32 \&file, defining two vectors ij and jk. The rotational ACF
33 \&is calculated as the autocorrelation function of the vector
34 \&n = ij x jk, i.e. the cross product of the two vectors.
35 \&Since three atoms span a plane, the order of the three atoms
36 \&does not matter. Optionally, controlled by the \fB \-d\fR switch, you can
37 \&calculate the rotational correlation function for linear molecules
38 \&by specifying two atoms (i,j) in the index file.
45 \&\fB g_rotacf \-P 1 \-nparm 2 \-fft \-n index \-o rotacf\-x\-P1
46 \&\-fa expfit\-x\-P1 \-beginfit 2.5 \-endfit 20.0\fR
49 \&This will calculate the rotational correlation function using a first
50 \&order Legendre polynomial of the angle of a vector defined by the index
51 \&file. The correlation function will be fitted from 2.5 ps until 20.0 ps
52 \&to a two\-parameter exponential.
56 Trajectory: xtc trr trj gro g96 pdb cpt
58 .BI "\-s" " topol.tpr"
60 Run input file: tpr tpb tpa
62 .BI "\-n" " index.ndx"
66 .BI "\-o" " rotacf.xvg"
72 Print help info and quit
74 .BI "\-[no]version" "no "
75 Print version info and quit
77 .BI "\-nice" " int" " 19"
80 .BI "\-b" " time" " 0 "
81 First frame (ps) to read from trajectory
83 .BI "\-e" " time" " 0 "
84 Last frame (ps) to read from trajectory
86 .BI "\-dt" " time" " 0 "
87 Only use frame when t MOD dt = first time (ps)
90 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
92 .BI "\-xvg" " enum" " xmgrace"
93 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
96 Use index doublets (vectors) for correlation function instead of triplets (planes)
98 .BI "\-[no]aver" "yes "
99 Average over molecules
101 .BI "\-acflen" " int" " \-1"
102 Length of the ACF, default is half the number of frames
104 .BI "\-[no]normalize" "yes "
107 .BI "\-P" " enum" " 0"
108 Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR
110 .BI "\-fitfn" " enum" " none"
111 Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
113 .BI "\-ncskip" " int" " 0"
114 Skip N points in the output file of correlation functions
116 .BI "\-beginfit" " real" " 0 "
117 Time where to begin the exponential fit of the correlation function
119 .BI "\-endfit" " real" " \-1 "
120 Time where to end the exponential fit of the correlation function, \-1 is until the end
125 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.