1GMX-ROTACF(1)                       GROMACS                      GMX-ROTACF(1)
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NAME

6       gmx-rotacf  -  Calculate  the rotational correlation function for mole‐
7       cules
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SYNOPSIS

10          gmx rotacf [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]]
11                     [-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
12                     [-[no]w] [-xvg <enum>] [-[no]d] [-[no]aver]
13                     [-acflen <int>] [-[no]normalize] [-P <enum>]
14                     [-fitfn <enum>] [-beginfit <real>] [-endfit <real>]
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DESCRIPTION

17       gmx rotacf calculates the rotational  correlation  function  for  mole‐
18       cules.  Atom triplets (i,j,k) must be given in the index file, defining
19       two vectors ij and jk. The rotational ACF is calculated as the autocor‐
20       relation  function of the vector n = ij x jk, i.e. the cross product of
21       the two vectors.  Since three atoms span a  plane,  the  order  of  the
22       three atoms does not matter. Optionally, by invoking the -d switch, you
23       can calculate the rotational correlation function for linear  molecules
24       by specifying atom pairs (i,j) in the index file.
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26       EXAMPLES
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28       gmx  rotacf  -P 1 -nparm 2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1
29       -beginfit 2.5 -endfit 20.0
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31       This will calculate the rotational correlation function using  a  first
32       order Legendre polynomial of the angle of a vector defined by the index
33       file. The correlation function will be fitted from 2.5 ps until 20.0 ps
34       to a two-parameter exponential.
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OPTIONS

37       Options to specify input files:
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39       -f [<.xtc/.trr/…>] (traj.xtc)
40              Trajectory: xtc trr cpt gro g96 pdb tng
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42       -s [<.tpr>] (topol.tpr)
43              Portable xdr run input file
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45       -n [<.ndx>] (index.ndx)
46              Index file
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48       Options to specify output files:
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50       -o [<.xvg>] (rotacf.xvg)
51              xvgr/xmgr file
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53       Other options:
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55       -b <time> (0)
56              Time of first frame to read from trajectory (default unit ps)
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58       -e <time> (0)
59              Time of last frame to read from trajectory (default unit ps)
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61       -dt <time> (0)
62              Only use frame when t MOD dt = first time (default unit ps)
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64       -[no]w (no)
65              View output .xvg, .xpm, .eps and .pdb files
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67       -xvg <enum> (xmgrace)
68              xvg plot formatting: xmgrace, xmgr, none
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70       -[no]d (no)
71              Use index doublets (vectors) for correlation function instead of
72              triplets (planes)
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74       -[no]aver (yes)
75              Average over molecules
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77       -acflen <int> (-1)
78              Length of the ACF, default is half the number of frames
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80       -[no]normalize (yes)
81              Normalize ACF
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83       -P <enum> (0)
84              Order of Legendre polynomial for ACF (0 indicates none):  0,  1,
85              2, 3
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87       -fitfn <enum> (none)
88              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
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90       -beginfit <real> (0)
91              Time where to begin the exponential fit of the correlation func‐
92              tion
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94       -endfit <real> (-1)
95              Time where to end the exponential fit of the  correlation  func‐
96              tion, -1 is until the end
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SEE ALSO

99       gmx(1)
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101       More     information    about    GROMACS    is    available    at    <‐
102       http://www.gromacs.org/>.
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105       2019, GROMACS development team
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1102019.2                           Apr 16, 2019                    GMX-ROTACF(1)
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