![\"Gaussian](\"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-content\/uploads\/sites\/1385\/2023\/09\/wcms1521-toc-0001-m.jpg\")
<\/p>\nGaussian accelerated molecular dynamics (GaMD) is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth biomolecular potential energy surface and reduce energy barriers. GaMD greatly accelerates biomolecular simulations by orders of magnitude. Without the need to set predefined reaction coordinates or collective variables, GaMD provides unconstrained enhanced sampling and is advantageous for simulating complex biological processes. The GaMD boost potential exhibits a Gaussian distribution, thereby allowing for energetic reweighting via cumulant expansion to the second order (i.e., \u201cGaussian approximation\u201d). This leads to accurate reconstruction of free energy landscapes of biomolecules. Hybrid schemes with other enhanced sampling methods, such as the replica exchange GaMD (rex-GaMD) and replica exchange umbrella sampling GaMD (GaREUS), have been introduced, further improving sampling and free energy calculations. Building on robust GaMD, we have developed novel \u201cSelective GaMD\u201d algorithms, including Ligand GaMD (LiGaMD), Peptide GaMD (Pep-GaMD) and Protein-Protein Interaction GaMD (PPI-GaMD). These new algorithms allow for repetitive dissociation and binding of small-molecule ligands, flexible peptides and proteins in unprecedented microsecond-timescale atomistic simulations. GaMD was successfully demonstrated on biomolecular simulations and revealed physical pathways and mechanisms of protein folding and ligand binding, which were consistent with experiments and long-timescale conventional MD simulations. GaMD has been implemented in the widely used AMBER, NAMD, GENESIS, OpenMM and Tinker-HP simulation packages. Applications of GaMD have revealed mechanisms of protein folding and conformational changes, ligand binding, protein-protein\/membrane\/nucleic acid interactions and carbohydrate dynamics.<\/p>\n
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Wang J, Arantes P, Bhattarai A, Hsu R, Pawnikar S, Huang Y-M, Palermo G* and Miao Y* (2021) Gaussian accelerated molecular dynamics: principles and applications.<\/a> WIREs Computational Molecular Science: e1521. Pang, Y.T.#, Y. Miao#,*, Y. Wang* and J. A. McCammon* (2017) Gaussian accelerated molecular dynamics in NAMD,<\/a> J Chemical Theory and Computation, 13(1): 9-19.<\/p>\n Miao, Y.*, Feher V. and McCammon JA (2015) Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation.<\/a> J Chemical Theory and Computation, 11(8): 3584-3595.<\/p>\n","protected":false},"excerpt":{"rendered":" Gaussian accelerated molecular dynamics (GaMD) Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for simultaneous unconstrained enhanced sampling and free energy calculations of biomolecules. It works by adding a harmonic boost potential to smooth biomolecular potential energy surface and reduce energy barriers. GaMD greatly accelerates biomolecular simulations by orders of magnitude. Without the … Read more<\/a><\/p>\n","protected":false},"author":22429,"featured_media":0,"parent":2507,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"layout":"","cellInformation":"","apiCallInformation":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2390","page","type-page","status-publish","hentry","odd"],"acf":[],"_links_to":[],"_links_to_target":[],"_links":{"self":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2390","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/users\/22429"}],"replies":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/comments?post=2390"}],"version-history":[{"count":2,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2390\/revisions"}],"predecessor-version":[{"id":3316,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2390\/revisions\/3316"}],"up":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2507"}],"wp:attachment":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/media?parent=2390"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
\n\u2022 Advanced Science News: A \u201ctime-accelerated computational microscope\u201d provides biologists with powerful insights<\/a><\/p>\n