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Accepted (AM)Open Access (License Unspecified), Open
Journal article
Optimizing String Method's Reproducibility Using Generalized Solute Tempering Replica Exchange
The journal of physical chemistry. B, v 125(24), pp 6609-6616
24 Jun 2021
PMID: 34110824
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Obtaining accurate and reproducible free energies from molecular simulations is somewhat tricky due to incomplete knowledge of crucial slow degrees of freedom leading to hidden barriers that can stymie sampling. Employing a sufficiently large number of collective variables (CV) and ensuring ergodic sampling in orthogonal CV space, perhaps via tempering methods, can reduce these issues to some extent. For complex systems with high-dimensional free energy landscapes, both these approaches become computationally expensive. For high-dimensional landscapes, efficient exploration can be enabled by using temperature-accelerated MD (TAMD) and identification and characterization of minimum free energy pathways connecting minima can be found by using the string method (SM). Both TAMD and SM use mean-force estimates from finite MD simulations and are thus susceptible to sampling restrictions from hidden variables. A recent development in parallel tempering methods, "generalized replica exchange solute tempering" (gREST), can enhance sampling at a reasonable computational cost with its flexibility to target very specific "solutes" which can include arbitrary independent variables. Considering the advantages of both methods, we implement gREST-enabled TAMD and SM. By considering two different collective variable representations of the pentapeptide neurotransmitter met-enkephalin, we show that both gREST-enabled TAMD and SM yield more accurate and reproducible free energy predictions than TAMD and SM alone. Given the moderate computational cost of gREST compared with other replica-exchange methods, gREST-enabled SM represents a more attractive method for characterizing free energy minima and pathways among them for a large variety of systems.
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Details
- Title
- Optimizing String Method's Reproducibility Using Generalized Solute Tempering Replica Exchange
- Creators
- Gourav Shrivastav - Drexel UniversityCameron F. Abrams - Drexel University
- Publication Details
- The journal of physical chemistry. B, v 125(24), pp 6609-6616
- Publisher
- American Chemical Society; Washington, DC
- Number of pages
- 8
- Grant note
- ACI-15485862 / National Science Foundation; National Science Foundation (NSF) R01-GM-100472 / National Institutes of Health; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Chemical and Biological Engineering
- Web of Science ID
- WOS:000668345100020
- Scopus ID
- 2-s2.0-85108669091
- Other Identifier
- 991019168967504721
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Data related to this publication, from InCites Benchmarking & Analytics tool:
- Web of Science research areas
- Chemistry, Physical