Free energy calculation using space filled design and weighted reconstruction: A modified single sweep approach
- Post by: Cameron Abrams
- November 18, 2019
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Anindya Bhaduri, Jasmine Gardner, CFA, and Lori Brady
Mol. Sim. 2019;46:193-206 (10.1080/08927022.2019.1688325)
Abstract: A modified single sweep approach is proposed for generating free energy landscapes. The approach replaces the use of temperature-accelerated molecular dynamics (TAMD) to generate centres in collective variable (CV) space at which mean forces are computed using restrained molecular dynamics (MD) simulations with a sequential space-filling design. This approach also modifies the radial basis function reconstruction step of the traditional single sweep approach and proposes a weighted reconstruction of the free energy surface using the previously generated mean forces. The modified approach is compared to the traditional single sweep (SS) approach on the (φ, ψ) dihedral free-energy map of solvated alanine dipeptide (AD). It is found that the new approach results in a more accurate reconstructed free energy than does the traditional approach when compared to the directly-computed reference free energy landscape. It is shown that the increased accuracy of the overall map stems from the improved 1-dimensional space filling (projective) property of the proposed design compared to that of the TAMD generated centres. A further enhancement in the accuracy of the crucial lower energy regions is enabled by the introduction of weights in the reconstruction step that give more importance to lower energy-valued regions.