Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 7, Issue 10, Pages 3199-3207Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ct200430c
Keywords
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Funding
- National Science Foundation
- National Institutes of Health, Howard Hughes Medical Institute, Center for Theoretical Biological Physics
- National Biomedical Computation Resource
- NSF supercomputer centers
- Texas Advanced Computing Center [TG-MCA93S013, TG-MCB090187]
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Accelerated molecular dynamics (aMD) is an enhanced sampling technique that expedites conformational space sampling by reducing the barriers separating various low-energy states of a system. Here, we present the first application of the aMD method on lipid membranes. Altogether, similar to 1.5 mu s simulations were performed on three systems: a pure POPC bilayer, a pure DMPC bilayer, and a mixed POPC:DMPC bilayer. Overall, the aMD simulations are found to produce significant speedup in trans-gauche isomerization and lipid lateral diffusion versus those in conventional MD (cMD) simulations. Further comparison of a 70-ns aMD run and a 300-ns cMD run of the mixed POPC:DMPC bilayer shows that the two simulations yield similar lipid mixing behaviors, with aMD generating a 2-3-fold speedup compared to cMD. Our results demonstrate that the aMD method is an efficient approach for the study of bilayer structural and dynamic properties. On the basis of simulations of the three bilayer systems, we also discuss the impact of aMD parameters on various lipid properties, which can be used as a guideline for future aMD simulations of membrane systems.
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