QM MD

20 ps QM MD of Ubiquitin in explicit water

All-atom (12199 atoms) QM MD simulation in water droplet was performed on Ubiquitin protein.

Level of theory: PM3, spherical boundary potential, Nose-Hoover thermostat, T=310K

ChemPhysChem, 2009, 10 (18) 3194-3196

10 ps QM MD in implicit water

All-atom (1700 atoms) QM MD simulation was performed on complex of p56lck SH2 domain with Ac-pYEEI phosphopeptide (PDB id 1LKK).

Level of theory: PM3 / COSMO, Langevin dynamics, T=300K, 1 fs integration time step

Hardware: AMD Opteron 2.4 GHz, 2-CPUs

Calculation time: 1 month