[gmx-users] g_rotacf

[Stephanus Fengler]

Daniel K wrote:
> How should I change it so it calculates the 40 ps?
>
You need at least a 80ps trajectory otherwise you basically have too 
less  data to correlate with with a lag time of 40ps.
Check gromacs manual 4.0 at section 8.5
> On Wed, Oct 22, 2008 at 6:34 PM, Xavier Periole <X.Periole at rug.nl 
> <mailto:X.Periole at rug.nl>> wrote:
>
>     On Wed, 22 Oct 2008 17:38:58 -0400
>      "Daniel K" <chmdan at gmail.com <mailto: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
>     -----------------------------------------------------
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