Comparing the Efficiency of Biased and Unbiased Molecular Dynamics in Reconstructing the Free Energy Landscape of Met-Enkephalin
| Autor: | Ludovico Sutto, Marco D'Abramo, Francesco Luigi Gervasio |
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| Rok vydání: | 2010 |
| Předmět: |
Physics
Quantitative Biology::Biomolecules Metadynamics Energy landscape Scale (descriptive set theory) Potential energy Computer Science Applications Molecular dynamics Convergence (routing) Principal component analysis Statistical physics Physical and Theoretical Chemistry Simulation Eigenvalues and eigenvectors |
| Zdroj: | Journal of Chemical Theory and Computation. 6:3640-3646 |
| ISSN: | 1549-9626 1549-9618 |
| DOI: | 10.1021/ct100413b |
| Popis: | All-atom unbiased molecular dynamics simulations are now able to explore the microsecond to millisecond time scale for simple biological macromolecules in an explicit solvent. This allows for a careful comparison of the efficiency and accuracy of enhanced sampling methods versus long unbiased molecular dynamics in reconstructing conformational free energy surfaces. Here, we use an equilibrium microsecond-long molecular dynamics simulation as a reference to analyze the convergence properties of well-tempered metadynamics with two different sets of collective variables. In the case of the small and very diffusive Met-enkephalin pentapeptide, we find that the performance strongly depends on the choice of the collective variables (CVs). Using a set of principal component analysis derived eigenvectors, the convergence of the FES is faster than with both hand-picked CVs and unbiased molecular dynamics. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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