Subject: order parameters

From: Craig Shepherd <[email-masked]>
Date: Fri, 28 Mar 2003 01:40:56 -0700

Hello all,

I have a question regarding the calculation of 15N order parameters
> from an MD simulation of a protein.  I am familiar with the Lipari-Szabo
model, and realize that the order parameters can be calculated from the
limit of the auto-correlation function (of the 2nd Legendre polynomial) 
of the N-H bond vectors at infinite time, and that these should be 
calculated from protein structures which have been progressively fit to, 
say, the starting structure.

My question is: what method does one use to assure that the 
auto-correlation function for a given bond vector has converged to
some relatively constant value?  The few papers I've read in which
such calculations are performed don't seem to specify how this was
done (I read them all some time ago, so please forgive me if I am
wrong about this).

Any help you can give me on the convergence question (and any other 
nuances or details, including the ones I claim to "understand" in the 
first paragraph) would be welcome.

Thanks in advance,

Craig Shepherd