[gmx-users] auto correlation function and time

[Mohsen Ramezanpour]

Hi guys,

I have a quick question on calculating the autocorrelation time:

I have the file for a dihedral angle vs time (named angle.xvg).

Now, I need to calculate the autocorrelation time for this angle.

There are two problems, though:

1) If I use the angle.xvg with g_angle itself (i.e. using the -oc option),
the graph for the autocorrelation function is different than if I use
g_analyze -ac option.

Here are the commands I used:
gmx angle  -f  md.xtc   -n  index.ndx  -ov  test.xvg  -oc test-corr1.xvg
 -type dihedral

gmx analyze   -f  test.xvg    -ac  test-corr2.xvg


2) given the output, either test-corr1.xvg  or test-corr2.xvg, how can I
calculate the "correlation time" for this property? please consider that
this is an angle.

Googling, I found different things. One told to integrate the
autocorrelation function, and somewhere else, I found that I should first
fit the autocorrelation function with an exponential function and then take
the decay time as the correlation time.

Not sure what is the correct way to do it.

Thanks in advance for your reply and comments.

Cheers,
Mohsen

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