The Limitations of Temperature Replica Exchange (T-REMD) for Protein Folding

Friday, January 18, 2008 - 9:00am - 9:30am
EE/CS 3-180
Jed Pitera (IBM Research Division)
The replica exchange/parallel tempering method and its variations offer the
hope of
improved sampling for many challenging problems in molecular simulation.
Like all
sampling methods, however, the effectiveness of replica exchange is highly
on the specific physical system being studied. We have carried out large
temperature replica exchange (T-REMD) simulations of peptides and proteins
in explicit solvent
and encountered a number of issues that limit the effectiveness of the
method in sampling
biomolecular conformations. In particular, our results suggest the need
to either
replace or augment the temperature variable with an alternative extended
such as Hamiltonian scaling.
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