development

PI/MD :: Mixed Quantum/Classical method to perform Born-Oppenheimer molecular dynamics in ground and excited states. The method combines the PPP hamiltonian for pi-conjugated systems with the molecular mechanics model QCFF/PI.

F.Sterpone&PJ.Rossky, JPCB (2008),112,4983-4993

Population COLVAR :: New collective variable for monitoring the evolution of several chemical species in condensed matter reactions. The colvar is implemented in CP2K code along with the Temperature Accelerated MD technique.

F.Sterpone,S.Bonelle,S.Meloni, JPCC (2012),116, 19636-19643

IP/OPEP :: Effective potential to model ion-pairs in coarse-graining simulations. The potentials are developed via the Iterative Boltzmann inversion method.

F.Sterpone et al, JCTC (2013),9, 4574-4585

MUPHY/OPEP :: Multi-scale engine to couple the OPEP coarse-grained model for protein with hydrodynamics.

F.Sterpone et al, JCTC (2015), 11, 1843-1853

CLUSTERING :: Codes to perform conformational and kinetic clustering of protein structures [here] and Hydrogen Bond network connectivity states [here]. Author: M. Kalimeri [Personal Page].

O. Rahaman et al., J. Phys. Chem. B (2017) 121, 6792−6798.