期刊
JOURNAL OF CHEMICAL PHYSICS
卷 149, 期 7, 页码 -出版社
AMER INST PHYSICS
DOI: 10.1063/1.5027479
关键词
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资金
- National Science Foundation (NSF) [CHE-1565980]
- Swiss National Science Foundation [PA00P2 129092]
- Army Research Office (ARO) [W911NF-13-1-0387]
- York University Materials Research Science and Engineering Center (MRSEC) program of the NSF [DMR-1420073]
- Swiss National Science Foundation (SNF) [PA00P2_129092] Funding Source: Swiss National Science Foundation (SNF)
- Direct For Mathematical & Physical Scien
- Division Of Chemistry [1565980] Funding Source: National Science Foundation
A method for calculating the free energy difference between two structurally defined conformational states of a chemical system is developed. A path is defined using a previously reported collective variable that interpolates between two or more conformations, and a restraint is introduced in order to keep the system close to the path. The evolution of the system along the path, which typically presents a high free energy barrier, is generated using enhanced sampling schemes. Although the formulation of the method in terms of a path is quite general, an important advance in this work is the demonstration that prior knowledge of the path is, in fact, not needed and that the free energy difference can be obtained using a simplified definition of the path collective variable that only involves the endpoints. We first validate this method on cyclohexane isomerization. The method is then tested for an extensive conformational change in a realistic molecular system by calculating the free energy difference between the alpha-helix and beta-hairpin conformations of deca-alanine in solution. Finally, the method is applied to a biologically relevant system to calculate the free energy difference of an observed and a hypothetical conformation of an antigenic peptide bound to a major histocompatibility complex. Published by AIP Publishing.
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