1 .TH g_velacc 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
3 g_velacc - calculates velocity autocorrelation functions
9 .BI "\-s" " topol.tpr "
10 .BI "\-n" " index.ndx "
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_velacc\fR computes the velocity autocorrelation function.
31 \&When the \fB \-m\fR option is used, the momentum autocorrelation
32 \&function is calculated.
35 \&With option \fB \-mol\fR the velocity autocorrelation function of
36 \&molecules is calculated. In this case the index group should consist
37 \&of molecule numbers instead of atom numbers.
40 \&Be sure that your trajectory contains frames with velocity information
41 \&(i.e. \fB nstvout\fR was set in your original \fB .mdp\fR file),
42 \&and that the time interval between data collection points is
43 \&much shorter than the time scale of the autocorrelation.
47 Full precision trajectory: trr trj cpt
49 .BI "\-s" " topol.tpr"
51 Structure+mass(db): tpr tpb tpa gro g96 pdb
53 .BI "\-n" " index.ndx"
63 Print help info and quit
65 .BI "\-[no]version" "no "
66 Print version info and quit
68 .BI "\-nice" " int" " 19"
71 .BI "\-b" " time" " 0 "
72 First frame (ps) to read from trajectory
74 .BI "\-e" " time" " 0 "
75 Last frame (ps) to read from trajectory
77 .BI "\-dt" " time" " 0 "
78 Only use frame when t MOD dt = first time (ps)
81 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
83 .BI "\-xvg" " enum" " xmgrace"
84 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
87 Calculate the momentum autocorrelation function
90 Calculate the velocity acf of molecules
92 .BI "\-acflen" " int" " \-1"
93 Length of the ACF, default is half the number of frames
95 .BI "\-[no]normalize" "yes "
98 .BI "\-P" " enum" " 0"
99 Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR
101 .BI "\-fitfn" " enum" " none"
102 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
104 .BI "\-ncskip" " int" " 0"
105 Skip this many points in the output file of correlation functions
107 .BI "\-beginfit" " real" " 0 "
108 Time where to begin the exponential fit of the correlation function
110 .BI "\-endfit" " real" " \-1 "
111 Time where to end the exponential fit of the correlation function, \-1 is until the end
116 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.