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enhanced sampling without applying any biasing force
发布时间:2022-03-20

parallel cascade selection MD (PaCS-MD),

Dissociation Pathways of the p53 DNA Binding Domain from DNA
and Critical Roles of Key Residues Elucidated by dPaCS-MD/MSM
Mohamed Marzouk Sobeh and Akio Kitao *

J. Chem. Inf. Model. 2022, 62, 12941307

Harada, R.; Kitao, A. Parallel Cascade Selection Molecular

Dynamics (PaCS-MD) to Generate Conformational Transition
Pathway. J. Chem. Phys. 2013 , 139 , No. 035103.
Tran, D. P.; Takemura, K.; Kuwata, K.; Kitao, A. Protein-
Ligand Dissociation Simulated by Parallel Cascade Selection
Molecular Dynamics. J. Chem. Theory Comput. 2018 , 14 , 404 417.


milestoning

Vanden-Eijnden, E.; Venturoli, M. Markovian Milestoning with
Voronoi Tessellations. J. Chem. Phys. 2009 , 130 , 194101.
Vanden-Eijnden, E.; Venturoli, M.; Ciccotti, G.; Elber, R. On
the Assumptions Underlying Milestoning. J. Chem. Phys. 2008 , 129 ,
174102.


weighted ensemble,

https://livecomsjournal.org/index.php/livecoms/article/view/v1i2e10607


forward flux sampling

Allen, R. J.; Valeriani, C.; Rein Ten Wolde, P. Forward Flux
Sampling for Rare Event Simulations. J. Phys.: Condens. Matter 2009 ,
21 , No. 463102.