Paper Citing NAMD - Abstract
Faginas-Lago, Noelia; Alberti, Margarita; Costantini, Alessandro; Lagana, Antonio; Lombardi, Andrea; Pacifici, Leonardo
An innovative synergistic grid approach to the computational study of protein aggregation mechanisms
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2226, JUL 2014
Thanks to the advances in grid technologies, we are able to propose here an evolution of our molecular simulator that, when moving to larger systems, instead of reducing the granularity of the dynamical treatment (as is often done in molecular dynamics studies of such systems) exploits the extra power of the grid approach to the end of preserving the detailed nature of theatomistic formulation of the interaction. Key steps of such evolution are: (1) the assemblage of the interaction based on a composition of the ab initio intramolecular data and a portable parameterization of the intermolecular potential linking ab initio evaluation of intramolecular potentials and the partitioning of molecular polarizability; (2) the exploitation of an efficient coordinated porting and running of molecular dynamics codes on the European grid distributed computing infrastructure. As a prototype case study, the N-methylacetamide dimer in vacuo has been considered and the formation of possible conformers is analyzed.
