How should I change it so it calculates the 40 ps?<br><br><div class="gmail_quote">On Wed, Oct 22, 2008 at 6:34 PM, Xavier Periole <span dir="ltr"><<a href="mailto:X.Periole@rug.nl">X.Periole@rug.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">On Wed, 22 Oct 2008 17:38:58 -0400<br>
"Daniel K" <<a href="mailto:chmdan@gmail.com" target="_blank">chmdan@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I have been trying to use g_rotacf with a simulation run for 40 ps (20000)<br>
with steps of 2fs and the frames where extracted every 50 fs (25 frames).<br>
The trajectory file is correct because it has 801 frames. When I calculate<br>
the g_rotacf I only get 20 ps and the time step is 50 fs. Does any body no<br>
why?<br>
</blockquote></div>
What is wrong with this? By default g_rotacf plots only half of the time<br>
correlation function ...<br>
I do not know what you looking at but 40 ps is pretty short simulation.<div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
This is the header and end of the file that I get<br>
# This file was created Mon Oct 20 11:38:06 2008<br>
# by the following command:<br>
# g_rotacf -P 2 -f md_noT.trr -s md_noT.tpr -n NC.ndx -o md_noT_ACF.xvg -d<br>
#<br>
# g_rotacf is part of G R O M A C S:<br>
#<br>
# Glycine aRginine prOline Methionine Alanine Cystine Serine<br>
#<br>
@ title "Rotational Correlation Function"<br>
@ xaxis label "Time (ps)"<br>
@ yaxis label "C(t)"<br>
@TYPE xy<br>
0.000 1.00000<br>
0.050 0.95376<br>
0.100 0.90907<br>
....<br>
19.800 -0.22896<br>
19.850 -0.22921<br>
19.900 -0.23028<br>
19.950 -0.23078<br>
20.000 -0.23111<br>
&<br>
</blockquote>
<br></div>
-----------------------------------------------------<br>
XAvier Periole - PhD<br>
<br>
- Molecular Dynamics Group -<br>
NMR and Computation<br>
University of Groningen<br>
The Netherlands<br>
-----------------------------------------------------<br>
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</blockquote></div><br>