1GMX-VELACC(1)                       GROMACS                      GMX-VELACC(1)
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NAME

6       gmx-velacc - Calculate velocity autocorrelation functions
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SYNOPSIS

9          gmx velacc [-f [<.trr/.cpt/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                     [-o [<.xvg>]] [-os [<.xvg>]] [-b <time>] [-e <time>]
11                     [-dt <time>] [-[no]w] [-xvg <enum>] [-[no]m] [-[no]recip]
12                     [-[no]mol] [-acflen <int>] [-[no]normalize] [-P <enum>]
13                     [-fitfn <enum>] [-beginfit <real>] [-endfit <real>]
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DESCRIPTION

16       gmx velacc computes the velocity autocorrelation function.  When the -m
17       option is used, the momentum autocorrelation function is calculated.
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19       With option -mol the velocity autocorrelation function of molecules  is
20       calculated.  In  this  case  the index group should consist of molecule
21       numbers instead of atom numbers.
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23       By using option -os you can also extract  the  estimated  (vibrational)
24       power spectrum, which is the Fourier transform of the velocity autocor‐
25       relation function.  Be sure that your trajectory contains  frames  with
26       velocity information (i.e. nstvout was set in your original .mdp file),
27       and that the time interval  between  data  collection  points  is  much
28       shorter than the time scale of the autocorrelation.
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OPTIONS

31       Options to specify input files:
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33       -f [<.trr/.cpt/...>] (traj.trr)
34              Full precision trajectory: trr cpt tng
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36       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
37              Structure+mass(db): tpr gro g96 pdb brk ent
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39       -n [<.ndx>] (index.ndx) (Optional)
40              Index file
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42       Options to specify output files:
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44       -o [<.xvg>] (vac.xvg)
45              xvgr/xmgr file
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47       -os [<.xvg>] (spectrum.xvg) (Optional)
48              xvgr/xmgr file
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50       Other options:
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52       -b <time> (0)
53              Time of first frame to read from trajectory (default unit ps)
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55       -e <time> (0)
56              Time of last frame to read from trajectory (default unit ps)
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58       -dt <time> (0)
59              Only use frame when t MOD dt = first time (default unit ps)
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61       -[no]w (no)
62              View output .xvg, .xpm, .eps and .pdb files
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64       -xvg <enum> (xmgrace)
65              xvg plot formatting: xmgrace, xmgr, none
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67       -[no]m (no)
68              Calculate the momentum autocorrelation function
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70       -[no]recip (yes)
71              Use cm^-1 on X-axis instead of 1/ps for spectra.
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73       -[no]mol (no)
74              Calculate the velocity acf of molecules
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76       -acflen <int> (-1)
77              Length of the ACF, default is half the number of frames
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79       -[no]normalize (yes)
80              Normalize ACF
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82       -P <enum> (0)
83              Order  of  Legendre polynomial for ACF (0 indicates none): 0, 1,
84              2, 3
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86       -fitfn <enum> (none)
87              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
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89       -beginfit <real> (0)
90              Time where to begin the exponential fit of the correlation func‐
91              tion
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93       -endfit <real> (-1)
94              Time  where  to end the exponential fit of the correlation func‐
95              tion, -1 is until the end
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SEE ALSO

98       gmx(1)
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100       More    information    about    GROMACS    is    available    at     <‐
101       http://www.gromacs.org/>.
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104       2022, GROMACS development team
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1092022.3                           Sep 02, 2022                    GMX-VELACC(1)
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