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gmx-rotacf - Online in the Cloud

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This is the command gmx-rotacf that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gmx-rotacf - Calculate the rotational correlation function for molecules

SYNOPSIS


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

DESCRIPTION


gmx rotacf calculates the rotational correlation function for molecules. Atom triplets
(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, by invoking the -d switch, you can calculate the
rotational correlation function for linear molecules by specifying atom pairs (i,j) in the
index file.

EXAMPLES

gmx 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.

OPTIONS


Options to specify input files:

-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng

-s [<.tpr>] (topol.tpr)
Portable xdr run input file

-n [<.ndx>] (index.ndx)
Index file

Options to specify output files:

-o [<.xvg>] (rotacf.xvg)
xvgr/xmgr file

Other options:

-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]w (no)
View output .xvg, .xpm, .eps and .pdb files

-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none

-[no]d (no)
Use index doublets (vectors) for correlation function instead of triplets (planes)

-[no]aver (yes)
Average over molecules

-acflen <int> (-1)
Length of the ACF, default is half the number of frames

-[no]normalize (yes)
Normalize ACF

-P <enum> (0)
Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3

-fitfn <enum> (none)
Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9

-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

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