Jeffrey Comer, James Phillips, Klaus Schulten, and Christophe Chipot.
Multiple-replica strategies for free-energy calculations in NAMD:
Multiple-walker adaptive biasing force and walker selection rules.
Journal of Chemical Theory and Computation, 10:5276-5285,
2014.
COME2014B
From the most powerful supercomputers to multicore desktops and laptops, parallel
computing architectures have been in the mainstream for some time. However, numerical
schemes for calculating free energies in molecular systems that directly leverage this
hardware paradigm, usually taking the form of multiple-replica strategies, are just now on
the cusp of becoming standard practice. Here, we present a modification of the popular
molecular dynamics program NAMD that is envisioned to facilitate the use of powerful
multiple-replica strategies to improve ergodic sampling for a specific class of free-energy
methods known as adaptive biasing force. We describe the software implementation in a
so-called multiple-walker context, alongside the interface that makes the proposed
approach accessible to the end users. We further evaluate the performance of the adaptive
biasing force multiple-walker strategy for a model system, namely the reversible folding of
a short peptide, and show, in particular in regions of the transition coordinate where
convergence of the free-energy calculation is encumbered by hidden barriers, that the
multiple-walker strategy can yield far more reliable results in appreciably less real time on
parallel architectures, relative to standard, single-replica calculations.
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