AMBER Archive (2007)

Subject: AMBER: correlation time

From: Tuncel, Aytug (atuncel_at_ad.wsu.edu)
Date: Tue Dec 04 2007 - 12:22:55 CST

Dear all,

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?

Thanks in advance

Aytug

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