dorsal/arxiv
View SchemaEfficient use of non-equilibrium measurement to estimate free energy differences for molecular systems
| Authors | F. Marty Ytreberg, Daniel M. Zuckerman |
|---|---|
| Categories | |
| ArXiv ID | physics/0402065 |
| URL | https://arxiv.org/abs/physics/0402065 |
Abstract
A promising method for calculating free energy differences Delta F is to generate non-equilibrium data via ``fast-growth'' simulations or experiments -- and then use Jarzynski's equality. However, a difficulty with using Jarzynski's equality is that Delta F estimates converge very slowly and unreliably due to the nonlinear nature of the calculation -- thus requiring large, costly data sets. Here, we present new analyses of non-equilibrium data from various simulated molecular systems exploiting statistical properties of Jarzynski's equality. Using a fully automated procedure, with no user-input parameters, our results suggest that good estimates of Delta F can be obtained using 6-15 fold less data than was previously possible. Systematizing and extending previous work [1], the new results exploit the systematic behavior of bias due to finite sample size. A key innovation is better use of the more statistically reliable information available from the raw data.
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"abstract": "A promising method for calculating free energy differences Delta F is to\ngenerate non-equilibrium data via ``fast-growth\u0027\u0027 simulations or experiments --\nand then use Jarzynski\u0027s equality. However, a difficulty with using Jarzynski\u0027s\nequality is that Delta F estimates converge very slowly and unreliably due to\nthe nonlinear nature of the calculation -- thus requiring large, costly data\nsets. Here, we present new analyses of non-equilibrium data from various\nsimulated molecular systems exploiting statistical properties of Jarzynski\u0027s\nequality. Using a fully automated procedure, with no user-input parameters, our\nresults suggest that good estimates of Delta F can be obtained using 6-15 fold\nless data than was previously possible. Systematizing and extending previous\nwork [1], the new results exploit the systematic behavior of bias due to finite\nsample size. A key innovation is better use of the more statistically reliable\ninformation available from the raw data.",
"arxiv_id": "physics/0402065",
"authors": [
"F. Marty Ytreberg",
"Daniel M. Zuckerman"
],
"categories": [
"physics.comp-ph",
"physics.bio-ph"
],
"title": "Efficient use of non-equilibrium measurement to estimate free energy differences for molecular systems",
"url": "https://arxiv.org/abs/physics/0402065"
},
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