Re: [AMBER] nmr order parameter and autocorrelation

From: Paul S. Nerenberg <>
Date: Fri, 30 Apr 2010 15:19:51 -0700


Your e-mail is unclear in terms of what you mean by "negative value of
the auto-correlation function". It is not unexpected that the auto-
correlation function becomes negative at some correlation time (tau),
although it should usually be fluctuating around zero when this
happens (i.e., not reaching a large negative value). Moreover, if you
were to average your C(tau) calculation over several trajectories,
then you should see that these fluctuations about zero generally
become smaller (as this "noise" is averaged out).

So long as your simulations are adequate in length with regards to the
max. correlation time and you are reasonably certain that your system
can be analyzed with the model-free approach (which is nothing more
than a *model* that makes assumptions about the dynamics of your
molecule), then you should not have a problem fitting your auto-
correlation functions to that exponential form.



P.S. The max. correlation time used in your analysis (and
correspondingly your simulation length) should always be chosen with
regard to the characteristic relaxation times of your molecule, as is
explicitly demonstrated in the article that Carlos referenced. I'm
sure that the more NMR-minded AMBER users out there probably have some
other pointers as well...

On Apr 30, 2010, at 2:39 PM, wrote:

> Thanks for the information. I read the Bruschweiler paper for the
> IRED method and think it is OK to not use IRED approach. The
> question still remains.
> Quoting Carlos Simmerling <>:
>> this is a useful article for such calculations
>> On Fri, Apr 30, 2010 at 4:43 PM, <> wrote:
>>> According to model-free formalism, the internal correlation
>>> function of NH
>>> vector, CI(t)=S^2+(1-S^2)e^(-t/tau)>=0. I tried to calculate the
>>> order
>>> parameter from MD calculation. However, I got negative value of the
>>> auto-correlation function for some residues. Is the defination of
>>> autocorrelation different between NMR and MD? Thanks.
>>> _______________________________________________
>>> AMBER mailing list
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Received on Fri Apr 30 2010 - 15:30:03 PDT
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