Page - 15 - in Charge Transport in DNA - Insights from Simulations

2.2MolecularDynamicsSimulation which makes simulations on the desired time scales computationally more demanding • Second, fast motions in the system have to be accounted for. The fastest motion in a biomolecular system is the C-H bond stretching with a period of about 10 fs. A rule of thumb recommends the step size to be one order ofmagnitude smaller than this fastestmotion. This normally leads to a time stepof1 fs inMDsimulationsofbiomolecules. Biomolecular processes, like protein folding, happenon thenano- tomicrosecond or even longer time scales typically. Millions ofMD integration steps have to be performed to reach these timescales,whichmakes the computational efficiencyof every time step very important. The calculation of forces takes the larges amount of the computational time (99%oreevenmore) in every time step. There aremore sophisticated integrationmethodswhichallowa larger timestepswithout increas- ing thenumerical error, buton theotherhand,morecomputational time isneeded per step. Therefore, an MD simulation is possible with a chosen integration method and a given force field. In order to perform simulations resembling the experimental setupor even thenatural environment, thermodynamic ensembles are introduced. 2.2.2 ThermodynamicEnsembles Theconceptually simplest ensemble is themicro-canonical ensemble (NVE)where the number of particles (N), the volume of the simulation box (V) and the total energy (E) are held constant. As the total energy is conserved, the temperature in the system can be very different in place and time. This is not the situation in a physical systeminequilibriumwith theenvironment. Toachieve this, temperature andpressure couplingsare introduced. TemperatureCoupling ThecanonicalensemblecoupledtoanexternalheatbathiscalledNVTensemble.A commonway todescribe thebath is theBerendsen thermostat [57]. Anydeviation 15