Configurational space discretization and free energy calculation in complex molecular systems.

ABSTRACT: We sought to design a free energy calculation scheme with the hope of saving cost for generating dynamical information that is inherent in trajectories. We demonstrated that snapshots in a converged trajectory set are associated with implicit conformers that have invariant statistical weight distribution (ISWD). Since infinite number of sets of implicit conformers with ISWD may be created through independent converged trajectory sets, we hypothesized that explicit conformers with ISWD may be constructed for complex molecular systems through systematic increase of conformer fineness, and tested the hypothesis in lipid molecule palmitoyloleoylphosphatidylcholine (POPC). Furthermore, when explicit conformers with ISWD were utilized as basic states to define conformational entropy, change of which between two given macrostates was found to be equivalent to change of free energy except a mere difference of a negative temperature factor, and change of enthalpy essentially cancels corresponding change of average intra-conformer entropy. By implicitly taking advantage of entropy enthalpy compensation and forgoing all dynamical information, constructing explicit conformers with ISWD and counting thermally accessible number of which for interested end macrostates is likely to be an efficient and reliable alternative end point free energy calculation strategy.

SUBMITTER: Wang K 

PROVIDER: S-EPMC4790156 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature