[gmx-users] g_rotacf

[Xavier Periole]

On Wed, 22 Oct 2008 17:38:58 -0400
  "Daniel K" <chmdan at gmail.com> wrote:
> I have been trying to use g_rotacf with a simulation run for 40 ps (20000)
> with steps of 2fs and the frames where extracted every 50 fs (25 frames).
> The trajectory file is correct because it has 801 frames. When I calculate
> the g_rotacf I only get 20 ps and the time step is 50 fs. Does any body no
> why?
What is wrong with this? By default g_rotacf plots only half of the time
correlation function ...
I do not know what you looking at but 40 ps is pretty short simulation.
  
> This is the header and end of the file that I get
> # This file was created Mon Oct 20 11:38:06 2008
> # by the following command:
> # g_rotacf -P 2 -f md_noT.trr -s md_noT.tpr -n NC.ndx -o md_noT_ACF.xvg -d
> #
> # g_rotacf is part of G R O M A C S:
> #
> # Glycine aRginine prOline Methionine Alanine Cystine Serine
> #
> @    title "Rotational Correlation Function"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "C(t)"
> @TYPE xy
>     0.000     1.00000
>     0.050     0.95376
>     0.100     0.90907
>  ....
>    19.800    -0.22896
>    19.850    -0.22921
>    19.900    -0.23028
>    19.950    -0.23078
>    20.000    -0.23111
> &

-----------------------------------------------------
XAvier Periole - PhD

- Molecular Dynamics Group -
NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------