AMBER Archive (2007)

Subject: RE: AMBER: correlation time

From: Tuncel, Aytug (atuncel_at_ad.wsu.edu)
Date: Thu Dec 06 2007 - 03:44:29 CST

Thanks for your answer Dr. Case. By "enthalpy" do you mean the delta_G or individual energies of complex, receptor and ligand?
Does the correlation time for relaxation of effective energy fluctuations correspond to the time where the correlation function "curve" reaches the zero value or do you use a threshold value?

Thanks in advance.

Aytug

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of David A. Case
Sent: Tue 12/4/2007 10:40 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: correlation time
 
On Tue, Dec 04, 2007, Tuncel, Aytug wrote:
>
> In the "Gohlke H, Kiel C, Case DA. Insights into protein-protein binding
> by binding free energy calculation and free energy decomposition for the
> Ras-Raf and Ras-RalGDS complexes. J Mol Biol. 2003 Jul
> 18;330(4):891-913" paper there is a section:
> " ... the energy values obtained for 150 adjacent snapshots extracted
> from 3 ns of production runs should be nearly uncorrelated, since the
> correlation times for relaxation of effective energy ?uctuations (1 ps)
> are shorter than the time-interval (20 ps) used for snapshot
> extraction."
>
> I wonder how the correlation time is calculated (how is the 1 ps value
> calculated), or how can we find that the extracted snapshots are
> uncorrelated?
>

You just take the MM-PBSA enthalpy estimate time series, and compute an
autocorrelation on it, using your favorite program. I think we used xmgrace
for this purpose, but many other stat programs will do the same thing. Or,
write your own perl or awk script, and you will have the added benefit of
really learning how this is done.

...dac
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu