Abstract
Molecular dynamics simulations of the RN24 peptide, which includes a
diverse set of structurally heterogeneous states, are carried out in
explicit solvent. Two approaches are employed and compared directly
under identical simulation conditions. Specifically, we examine
sampling by two individual long trajectories (microsecond timescale)
and many shorter (MS) uncoupled trajectories. Statistical analysis of
the structural properties indicates a qualitative agreement between
these approaches. Microsecond timescale sampling gives large
uncertainties on most structural metrics, while the shorter timescale
of MS simulations results in slight structural memory for
beta-structure starting states. Additionally, MS sampling detects
numerous transitions on a relatively short timescale that are not
observed in microsecond sampling, while long simulations allow for
detection of a few transitions on significantly longer timescales. A
correlation between the complex free energy landscape and the kinetics
of the equilibrium is highlighted by principal component analysis on
both simulation sets. This report highlights the increased precision of
the MS approach when studying the kinetics of complex conformational
change, while revealing the complementary insight and qualitative
agreement offered by far fewer individual simulations on significantly
longer timescales. (c) 2008 Wiley Periodicals, Inc.
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