[gmx-users] g_rotacf

[Daniel K]

How should I change it so it calculates the 40 ps?

On Wed, Oct 22, 2008 at 6:34 PM, Xavier Periole <X.Periole at rug.nl> wrote:

> 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
> -----------------------------------------------------
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