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dc.contributor.authorOzer, Gungor
dc.contributor.authorQuirk, Stephen
dc.contributor.authorHernandez, Rigoberto
dc.date.accessioned2012-12-04T23:49:17Z
dc.date.available2012-12-04T23:49:17Z
dc.date.issued2012-06
dc.identifier.citationOzer, Gungor; Quirk, Stephen and Hernandez, Rigoberto, "Adaptive steered molecular dynamics: Validation of the selection criterion and benchmarking energetics in vacuum," Journal of Chemical Physics, 136, 21, (June 7 2012).en_US
dc.identifier.issn1931-9223 (online)
dc.identifier.urihttp://hdl.handle.net/1853/45496
dc.description© 2012 American Institute of Physics. The electronic version of this article is the complete one and can be found at: http://dx.doi.org/10.1063/1.4725183en_US
dc.descriptionDOI: 10.1063/1.4725183
dc.description.abstractThe potential of mean force (PMF) for stretching decaalanine in vacuum was determined earlier by Park and Schulten [J. Chem. Phys. 120, 5946 (2004)] in a landmark article demonstrating the efficacy of combining steered molecular dynamics and Jarzynski's nonequilibrium relation. In this study, the recently developed adaptive steered molecular dynamics (ASMD) algorithm [G. Ozer, E. Valeev, S. Quirk, and R. Hernandez, J. Chem. Theory Comput. 6, 3026 (2010)] is used to reproduce the PMF of the unraveling of decaalanine in vacuum by averaging over fewer nonequilibrium trajectories. The efficiency and accuracy of the method are demonstrated through the agreement with the earlier work by Park and Schulten, a series of convergence checks compared to alternate SMD pulling strategies, and an analytical proof. The nonequilibrium trajectories obtained through ASMD have also been used to analyze the intrapeptide hydrogen bonds along the stretching coordinate. As the decaalanine helix is stretched, the initially stabilized i → i + 4 contacts (α-helix) is replaced by i → i + 3 contacts (310[subscript]-helix). No significant formation of i → i + 5 hydrogen bonds (π-helix) is observed.en_US
dc.language.isoen_USen_US
dc.publisherGeorgia Institute of Technologyen_US
dc.subjectConvergenceen_US
dc.subjectHydrogen bondsen_US
dc.subjectMolecular biophysicsen_US
dc.subjectMolecular configurationsen_US
dc.subjectMolecular dynamics methoden_US
dc.subjectProteinsen_US
dc.titleAdaptive steered molecular dynamics: Validation of the selection criterion and benchmarking energetics in vacuumen_US
dc.typeArticleen_US
dc.contributor.corporatenameGeorgia Institute of Technology. Center for Organic Photonics and Electronics
dc.contributor.corporatenameGeorgia Institute of Technology. Center for Computational Molecular Science and Technology
dc.contributor.corporatenameKimberly-Clark Corporation
dc.publisher.originalAmerican Institute of Physics
dc.identifier.doi10.1063/1.4725183


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