gamd<\/strong> YES \/ NO boost<\/strong> YES \/ NO boost_type<\/strong> DUAL \/ DIHEDRAL \/ POTENTIAL thresh_type<\/strong> LOWER \/ HIGHER update_period<\/strong> Integer sigma0_pot<\/strong> Real pot_max<\/strong> Real pot_min<\/strong> Real pot_ave<\/strong> Real pot_dev<\/strong> Real sigma0_dih<\/strong> Real dih_max<\/strong> Real dih_min<\/strong> Real dih_ave<\/strong> Real dih_dev<\/strong> Real NOTE: Please refer to the GENESIS user manual<\/a> for more detailed description.<\/p>\n H. Oshima, S. Re, Y. Sugita, Replica-Exchange Umbrella Sampling Combined with Gaussian Accelerated Molecular Dynamics for Free-Energy Calculation of Biomolecules. J Chem Theory Comput<\/em> 15, 5199-5208 (2019).<\/p>\n","protected":false},"excerpt":{"rendered":" Simulation Parameter Settings gamd YES \/ NO Default : NO Enable the GaMD method. boost YES \/ NO Default : YES Flag to apply GaMD boost to the system. If boost = NO, boost is not applied but GaMD parameters are updated from the trajectory. boost_type DUAL \/ DIHEDRAL \/ POTENTIAL Default: DUAL Type of … Read more<\/a><\/p>\n","protected":false},"author":22429,"featured_media":0,"parent":2390,"menu_order":10,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"layout":"","cellInformation":"","apiCallInformation":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2459","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\/2459","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=2459"}],"version-history":[{"count":0,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2459\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/pages\/2390"}],"wp:attachment":[{"href":"https:\/\/www.med.unc.edu\/pharm\/miaolab\/wp-json\/wp\/v2\/media?parent=2459"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}
\nDefault : NO
\nEnable the GaMD method.<\/p>\n
\nDefault : YES
\nFlag to apply GaMD boost to the system. If boost = NO, boost is not applied but GaMD parameters are updated from the trajectory.<\/p>\n
\nDefault: DUAL
\nType of boost.
\nDUAL: Boost is applied on both the dihedral and total potential energies.
\nDIHEDRAL: Boost is applied on only the dihedral energy.
\nPOTENTIAL: Boost is applied on only the total potential energy.<\/p>\n
\nDefault: LOWER Type of threshold.
\nLOWER: E is set to the lower bound E = Umax.
\nHIGHER: E is set to its upper bound E = Umin + 1\/k.<\/p>\n
\nDefault: 0
\nPeriod of updating parameters in units of time step.<\/p>\n
\nDefault: 6.0 (unit: kcal\/mol)
\nUpper limit of the standard deviation of the total potential boost that allows for accurate reweighting.<\/p>\n
\nDefault: -99999999.0 (unit: kcal\/mol)
\nMaximum of the total potential energy of the system.<\/p>\n
\nDefault: 99999999.0 (unit: kcal\/mol)
\nMinimum of the total potential energy of the system.<\/p>\n
\nDefault: 0.0 (unit: kcal\/mol)
\nAverage of the total potential energy of the system.<\/p>\n
\nDefault: 0.0 (unit: kcal\/mol)
\nStandard deviation of the total potential energy of the system.<\/p>\n
\nDefault: 6.0 (unit: kcal\/mol)
\nUpper limit of the standard deviation of the dihedral boost that allows for accurate reweighting.<\/p>\n
\nDefault: -99999999.0 (unit: kcal\/mol)
\nMaximum of the dihedral energy of the system.<\/p>\n
\nDefault: 99999999.0 (unit: kcal\/mol)
\nMinimum of the dihedral energy of the system.<\/p>\n
\nDefault: 0.0 (unit: kcal\/mol)
\nAverage of the dihedral energy of the system.<\/p>\n
\nDefault: 0.0 (unit: kcal\/mol)
\nStandard deviation of the dihedral energy of the system.<\/p>\nReference<\/h3>\n