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 <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
On Wed, 22 Oct 2008 17:38:58 -0400
"Daniel K" <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> 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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