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| Main Authors: | , , |
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| Format: | Preprint |
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2025
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| Online Access: | https://arxiv.org/abs/2501.08926 |
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| _version_ | 1866917893041553408 |
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| author | Mitra, Sudipta Biswas, Ranjit Chakrabarty, Suman |
| author_facet | Mitra, Sudipta Biswas, Ranjit Chakrabarty, Suman |
| contents | Estimating rare event kinetics from molecular dynamics simulations is a non-trivial task despite the great advances in enhanced sampling methods. Weighted Ensemble (WE) simulation, a special class of enhanced sampling techniques, offers a way to directly calculate kinetic rate constants from biased trajectories without the need to modify the underlying energy landscape using bias potentials. Conventional WE algorithms use different binning schemes to partition the collective variable (CV) space separating the two metastable states of interest. In this work, we have developed a new "binless" WE simulation algorithm to bypass the hurdles of optimizing binning procedures. Our proposed protocol (WeTICA) uses a low-dimensional CV space to drive the WE simulation toward the specified target state. We have applied this new algorithm to recover the unfolding kinetics of three proteins: (A) TC5b Trp-cage mutant, (B) TC10b Trp-cage mutant, and (C) Protein G, with unfolding times spanning the range between 3 and 40 μs using projections along predefined fixed Time-lagged Independent Component Analysis (TICA) eigenvectors as CVs. Calculated unfolding times converge to the reported values with good accuracy with more than one order of magnitude less cumulative WE simulation time than the unfolding time scales with or without a priori knowledge of the CVs that can capture unfolding. Our algorithm can be used with other linear CVs, not limited to TICA. Moreover, the new walker selection criteria for resampling employed in this algorithm can be used on more sophisticated nonlinear CV space for further improvements of binless WE methods. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2501_08926 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | WeTICA: A directed search weighted ensemble based enhanced sampling method to estimate rare event kinetics in a reduced dimensional space Mitra, Sudipta Biswas, Ranjit Chakrabarty, Suman Soft Condensed Matter Biological Physics Chemical Physics Computational Physics Estimating rare event kinetics from molecular dynamics simulations is a non-trivial task despite the great advances in enhanced sampling methods. Weighted Ensemble (WE) simulation, a special class of enhanced sampling techniques, offers a way to directly calculate kinetic rate constants from biased trajectories without the need to modify the underlying energy landscape using bias potentials. Conventional WE algorithms use different binning schemes to partition the collective variable (CV) space separating the two metastable states of interest. In this work, we have developed a new "binless" WE simulation algorithm to bypass the hurdles of optimizing binning procedures. Our proposed protocol (WeTICA) uses a low-dimensional CV space to drive the WE simulation toward the specified target state. We have applied this new algorithm to recover the unfolding kinetics of three proteins: (A) TC5b Trp-cage mutant, (B) TC10b Trp-cage mutant, and (C) Protein G, with unfolding times spanning the range between 3 and 40 μs using projections along predefined fixed Time-lagged Independent Component Analysis (TICA) eigenvectors as CVs. Calculated unfolding times converge to the reported values with good accuracy with more than one order of magnitude less cumulative WE simulation time than the unfolding time scales with or without a priori knowledge of the CVs that can capture unfolding. Our algorithm can be used with other linear CVs, not limited to TICA. Moreover, the new walker selection criteria for resampling employed in this algorithm can be used on more sophisticated nonlinear CV space for further improvements of binless WE methods. |
| title | WeTICA: A directed search weighted ensemble based enhanced sampling method to estimate rare event kinetics in a reduced dimensional space |
| topic | Soft Condensed Matter Biological Physics Chemical Physics Computational Physics |
| url | https://arxiv.org/abs/2501.08926 |