To access the full text documents, please follow this link: http://hdl.handle.net/2117/27226

Multiple active zones in hybrid QM/MM molecular dynamics simulations for large biomolecular systems
Torras Costa, Juan
Universitat Politècnica de Catalunya. Departament d'Enginyeria Química; Universitat Politècnica de Catalunya. IMEM - Innovació, Modelització i Enginyeria en (BIO) Materials
A new QM/MM molecular dynamics approach that can deal with the dynamics of large real systems involving several simultaneous active zones is presented. Multiple, unconnected but interacting quantum regions are treated independently in an ordinary QM/MM approach but in a manner which converges to a unique simulation. The multiple active zones in the hybrid QM/MM molecular dynamics methodology (maz-QM/MM MD) involve molecular dynamics that is driving the whole simulation with several parallel executions of energy gradients within the QM/MM approach that merge into each MD step. The Ewald-summation method is used to incorporate long-range electrostatic interactions among the active zones in conjunction with periodic boundary conditions. To illustrate and ascertain capabilities and limitations, we present several benchmark calculations using this approach. Our results show that the maz-QM/MM MD method is able to provide simultaneous treatment of several active zones of very large proteins such as the Cu-4His-¿C* cage, a self-assembly of a 24-mer cage-like protein ferritin
Àrees temàtiques de la UPC::Física::Física molecular
Molecular dynamics
Dinàmica molecular
info:eu-repo/semantics/publishedVersion
Article
         

Show full item record

Related documents

Other documents of the same author

Bendrea, Anca Dana; Fabregat Jové, Georgina; Torras Costa, Juan; Maione, Silvana; Cianga, Ioan; Valle Mendoza, Luis Javier del; Cianga, Luminita; Alemán Llansó, Carlos
Bertran Cànovas, Òscar; Curcó, David; Torras Costa, Juan; Ferreira, Carlos A.; Alemán Llansó, Carlos
Torras Costa, Juan; Bertran Cànovas, Òscar; Alemán Llansó, Carlos
Soto Delgado, Jorge; Torras Costa, Juan; Valle Mendoza, Luis Javier del; Estrany Coda, Francesc; Alemán Llansó, Carlos
Revilla López, Guillermo; Laurent,, Adele D.; Perpete, Eric A.; Jacquemin, Denis; Torras Costa, Juan; Assfeld, Xavier; Alemán Llansó, Carlos
 

Coordination

 

Supporters