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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

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

Wang Kai K Long Shiyang S Tian Pu P

Scientific reports 20160314

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 con ...[more]

PMID: 26974524

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Project description:The string method is a molecular-simulation technique that aims to calculate the minimum free-energy path of a chemical reaction or conformational transition, in the space of a pre-defined set of reaction coordinates that is typically highly dimensional. Any descriptor may be used as a reaction coordinate, but arguably the Cartesian coordinates of the atoms involved are the most unprejudiced and intuitive choice. Cartesian coordinates, however, present a non-trivial problem, in that they are not invariant to rigid-body molecular rotations and translations, which ideally ought to be unrestricted in the simulations. To overcome this difficulty, we reformulate the framework of the string method to integrate an on-the-fly structural-alignment algorithm. This approach, referred to as SOMA (String method with Optimal Molecular Alignment), enables the use of Cartesian reaction coordinates in freely tumbling molecular systems. In addition, this scheme permits the dissection of the free-energy change along the most probable path into individual atomic contributions, thus revealing the dominant mechanism of the simulated process. This detailed analysis also provides a physically-meaningful criterion to coarse-grain the representation of the path. To demonstrate the accuracy of the method we analyze the isomerization of the alanine dipeptide in vacuum and the chair-to-inverted-chair transition of ?-D mannose in explicit water. Notwithstanding the simplicity of these systems, the SOMA approach reveals novel insights into the atomic mechanism of these isomerizations. In both cases, we find that the dynamics and the energetics of these processes are controlled by interactions involving only a handful of atoms in each molecule. Consistent with this result, we show that a coarse-grained SOMA calculation defined in terms of these subsets of atoms yields nearidentical minimum free-energy paths and committor distributions to those obtained via a highly-dimensional string.

Project description:Entropy and the second law of thermodynamics are fundamental concepts that underlie all natural processes and patterns. Recent research has shown how the entropy of a landscape mosaic can be calculated using the Boltzmann equation, with the entropy of a lattice mosaic equal to the logarithm of the number of ways a lattice with a given dimensionality and number of classes can be arranged to produce the same total amount of edge between cells of different classes. However, that work seemed to also suggest that the feasibility of applying this method to real landscapes was limited due to intractably large numbers of possible arrangements of raster cells in large landscapes. Here I extend that work by showing that: (1) the proportion of arrangements rather than the number with a given amount of edge length provides a means to calculate unbiased relative configurational entropy, obviating the need to compute all possible configurations of a landscape lattice; (2) the edge lengths of randomized landscape mosaics are normally distributed, following the central limit theorem; and (3) given this normal distribution it is possible to fit parametric probability density functions to estimate the expected proportion of randomized configurations that have any given edge length, enabling the calculation of configurational entropy on any landscape regardless of size or number of classes. I evaluate the boundary limits (4) for this normal approximation for small landscapes with a small proportion of a minority class and show it holds under all realistic landscape conditions. I further (5) demonstrate that this relationship holds for a sample of real landscapes that vary in size, patch richness, and evenness of area in each cover type, and (6) I show that the mean and standard deviation of the normally distributed edge lengths can be predicted nearly perfectly as a function of the size, patch richness and diversity of a landscape. Finally, (7) I show that the configurational entropy of a landscape is highly related to the dimensionality of the landscape, the number of cover classes, the evenness of landscape composition across classes, and landscape heterogeneity. These advances provide a means for researchers to directly estimate the frequency distribution of all possible macrostates of any observed landscape, and then directly calculate the relative configurational entropy of the observed macrostate, and to understand the ecological meaning of different amounts of configurational entropy. These advances enable scientists to take configurational entropy from a concept to an applied tool to measure and compare the disorder of real landscapes with an objective and unbiased measure based on entropy and the second law.

Dataset Information

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

Publications

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

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