Journal article
Free energy calculation using space filled design and weighted reconstruction: a modified single sweep approach
Molecular simulation, v 46(3), pp 193-206
11 Feb 2020
Featured in Collection : UN Sustainable Development Goals @ Drexel
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.
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Details
- Title
- Free energy calculation using space filled design and weighted reconstruction: a modified single sweep approach
- Creators
- Anindya Bhaduri - Department of Civil Engineering, Johns Hopkins UniversityJasmine Gardner - Department of Chemistry - BMC, Uppsala UniversityCameron F Abrams - Department of Chemical and Biological Engineering, Drexel UniversityLori Graham-Brady - Department of Civil Engineering, Johns Hopkins University
- Publication Details
- Molecular simulation, v 46(3), pp 193-206
- Publisher
- Taylor & Francis
- Grant note
- W911NF-12-2-0022,W911NF-12-2-0023 / Army Research Laboratory (10.13039/100006754)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Chemical and Biological Engineering
- Web of Science ID
- WOS:000497038200001
- Scopus ID
- 2-s2.0-85075119584
- Other Identifier
- 991014969890704721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Chemistry, Physical
- Physics, Atomic, Molecular & Chemical