Journal of Computational Chemistry
Journal of Computational Chemistry
4 years ago

Efficacy of independence sampling in replica exchange simulations of ordered and disordered proteins

Efficacy of independence sampling in replica exchange simulations of ordered and disordered proteins
Jianhan Chen, Kuo Hao Lee
Recasting temperature replica exchange (T-RE) as a special case of Gibbs sampling has led to a simple and efficient scheme for enhanced mixing (Chodera and Shirts, J. Chem. Phys., 2011, 135, 194110). To critically examine if T-RE with independence sampling (T-REis) improves conformational sampling, we performed T-RE and T-REis simulations of ordered and disordered proteins using coarse-grained and atomistic models. The results demonstrate that T-REis effectively increase the replica mobility in temperatures space with minimal computational overhead, especially for folded proteins. However, enhanced mixing does not translate well into improved conformational sampling. The convergences of thermodynamic properties interested are similar, with slight improvements for T-REis of ordered systems. The study re-affirms the efficiency of T-RE does not appear to be limited by temperature diffusion, but by the inherent rates of spontaneous large-scale conformational re-arrangements. Due to its simplicity and efficacy of enhanced mixing, T-REis is expected to be more effective when incorporated with various Hamiltonian-RE protocols. © 2017 Wiley Periodicals, Inc. A simple extension of replica exchange (RE) involves multiple exchanges attempted at each exchange cycle with the same Metropolis criteria to enhance mixing. We performed atomistic and coarse-grained simulations of ordered and disordered proteins to critically examine if such temperature RE with independence sampling (T-REis) could improve conformational sampling. The results demonstrate that T-REis effectively increase the replica mobility in temperatures space; yet such enhanced mixing does not translate well into improved conformational sampling. The efficiency of T-RE does not appear to be limited by temperature diffusion, but by the inherent rates of spontaneous large-scale conformational re-arrangements.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1002/jcc.24923

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