期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 8, 期 11, 页码 4393-4404出版社
AMER CHEMICAL SOC
DOI: 10.1021/ct300512h
关键词
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资金
- NSF GRFP award
- Direct For Computer & Info Scie & Enginr
- Office of Advanced Cyberinfrastructure (OAC) [0910735] Funding Source: National Science Foundation
We evaluate the efficiency of the pH replica exchange molecular dynamics (pH-REMD) method proposed by Itoh et al. (Proteins 2011, 79, 3420-3436) by using it to predict the pK(a) values of the titratable residues in hen egg white lysozyme (HEWL). pK(a) values predicted using pH-REMD converge significantly faster than those calculated using constant pH molecular dynamics (CpHMD). Furthermore, increasing the frequency between exchange attempts in pH-REMD simulations improves protonation and conformational state sampling. By enabling the simulation to sample both conformational and protonation states more rapidly, pH-REMD simulations provide valuable insight into the pH-dependence of HEWL that the CpHMD simulations failed to capture. We present an efficient and highly scalable implementation of pH-REMD as an attractive enhancement to traditional CpHMD methods.
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