A comparison of pathway‐independent and pathway‐dependent methods in the calculation of conformational free enthalpy differences. (29th May 2015)

• Record Type: Journal Article
• Authors: Lin, Zhixiong; van Gunsteren, Wilfred F.
• Is Part Of: Protein science. Volume 25:Number 1(2016:Jan.)
• Page Start: 184
• Page End: 191
• Publication Date: 2015-05-29
• Subjects: molecular dynamics (MD) -- free enthalpy calculation -- conformational free enthalpy -- umbrella sampling -- β‐peptide; Proteins -- Periodicals; 572.6
• DOI: 10.1002/pro.2695
• Languages: English
• ISSNs: 0961-8368

Abstract

Abstract: The multistep umbrella sampling method, which belongs to pathway‐dependent methods to calculate conformational free enthalpy differences, is used to calculate the free enthalpy difference between a right‐handed 2.710/12 ‐helix and a left‐handed 314 ‐helix of a hexa‐β‐peptide in methanol solution. The same conformational free enthalpy difference was previously investigated using pathway‐independent methods such as direct counting and enveloping distribution sampling. Our results show that the pathway‐dependent simulations are sensitive to the choice of the pathway and its parameter values. A pathway based on restraining distances of hydrogen‐bonding atom pairs shows poor sampling for two different values of the restraining force constant. Another pathway based on restraining backbone dihedral angles did smoothly sample the transition between the two helical conformations, but only with a proper choice of the restraining force constant. The results illustrate that if, and only if, a proper pathway and proper parameters are chosen, the multistep umbrella sampling can be almost 50 times more efficient than the pathway‐independent methods in this case. The analysis illustrates the advantages and pitfalls of the much used multistep umbrella sampling methodology.