gmx rotacf¶
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)- Time of first frame to read from trajectory (default unit ps)
-e
<time> (0)- Time of last frame to read from trajectory (default unit ps)
-dt
<time> (0)- Only use frame when t MOD dt = first time (default unit ps)
-[no]w
(no)- View output .xvg, .xpm, .eps and .pdb files
-xvg
<enum> (xmgrace)- 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