August 7, 2012

All-atoms/Coarse-Grained model of DNA

Hybrid simulations of molecular systems combining all-atom (AA) with coarse grain (CG) representations are a valuable alternative to get atomistic details on relevant regions, while treating a bigger part of the system at the CG level. 
We developed a reduced set of parameters, which allows to easily link the AMBER force field of DNA with the CG representation developed by our group. 
No modification is needed for any of the existing residues (neither AA, nor CG). Only a reduced set of bonding interactions at the AA/CG interface is enough to produce a smooth transition of electrostatic, mechanic and dynamic features in different AA/CG systems using Generalized Born model for implicit solvent. 
All the interactions are computed within the same classical Hamiltonian. Therefore, it is straightforwardly usable in any popular simulation packages. 
This opens the possibility to an immediate extension multiscale quantum/ classical/CG simulation schemes.