Journal article
Method Evaluations for Adsorption Free Energy Calculations at the Solid/Water Interface through Metadynamics, Umbrella Sampling, and Jarzynski's Equality
Chemphyschem, v 19(6), pp 690-702
19 Mar 2018
PMID: 29265513
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Considerable interest in characterizing protein/peptide-surface interactions has prompted extensive computational studies on calculations of adsorption free energy. However, in many cases, each individual study has focused on the application of free energy calculations to a specific system; therefore, it is difficult to combine the results into a general picture for choosing an appropriate strategy for the system of interest. Herein, three well-established computational algorithms are systemically compared and evaluated to compute the adsorption free energy of small molecules on two representative surfaces. The results clearly demonstrate that the characteristics of studied interfacial systems have crucial effects on the accuracy and efficiency of the adsorption free energy calculations. For the hydrophobic surface, steered molecular dynamics exhibits the highest efficiency, which appears to be a favorable method of choice for enhanced sampling simulations. However, for the charged surface, only the umbrella sampling method has the ability to accurately explore the adsorption free energy surface. The affinity of the water layer to the surface significantly affects the performance of free energy calculation methods, especially at the region close to the surface. Therefore, a general principle of how to discriminate between methodological and sampling issues based on the interfacial characteristics of the system under investigation is proposed.
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Details
- Title
- Method Evaluations for Adsorption Free Energy Calculations at the Solid/Water Interface through Metadynamics, Umbrella Sampling, and Jarzynski's Equality
- Creators
- Qichao Wei - Nanjing Tech UniversityWeilong Zhao - University of AkronYang Yang - Drexel University, ChemistryBeiliang Cui - Nanjing Tech UniversityZhijun Xu - Nanjing Tech UniversityXiaoning Yang - Nanjing Tech University
- Publication Details
- Chemphyschem, v 19(6), pp 690-702
- Publisher
- Wiley
- Number of pages
- 13
- Grant note
- PBS0286 / Ohio Supercomputer Center 21606122 / National Natural Science Foundation of China; National Natural Science Foundation of China (NSFC) BK20160995 / Natural Science Foundation of Jiangsu Province
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Chemistry
- Web of Science ID
- WOS:000428380500002
- Scopus ID
- 2-s2.0-85041915566
- Other Identifier
- 991021874714804721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Chemistry, Physical
- Physics, Atomic, Molecular & Chemical