PN: Molecular Dynamics

• scenario: we have a structure / multiple structures of different points of a mechanism and we want to find out what happens in between

• we calculate the force acting on every atom depending on the position of all other atoms in the protein

Statistical mechanics

• we calculate microscopic simulations and try to get macroscopic properties out of it

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Probability distribution, describes how likely it is to find your system in a certain state.

Ensemble: Collection of all microscopic systems that belong to the same macroscopic state

Canonical ensemble: thermodynamic state with fixed N, V and E

Non-canonical ensemble: thermodynamic state with fixed N, V and T

N: number of electrons

V: volume

E: energy

T: temperature

• describes the interaction potential between the atoms of the molecules

• does not include motion

Determination of the potential energy function

• quantum chemical calculations (Hartree-Fock/DFT)

• refinement with experimental data

• …

You calculate positions of atoms and their velocity. You devide the time span you are interested in in small δt and recalculate positions and velocities.

The smaller δt, the better - but you are limited by your computational power: The smaller δt, the longer it takes.

• we cannot see H-bonds

• we cannot see bond formation and cleavage

  • QM/MM would be possible

• we cannot see excited states

• force-field inaccuracies

Generally, the accuracy/resolution is limited by the computational power. Calculating the potential energy function for each atom is very time-consuming.

• calculate for longer time steps

• SHAKE algorithm: constraint bond lengths

• coarse-grained models (instead of individual atoms)

• reduce number of interactions

-          to avoid just looking at a constrained volume (to avoid interactions/”bumps” of molecules with the borders), we use periodic cells – when one molecule exits on one side on the cell, it enters at the other side

Instead of calculating the force field for every individual atom, we summarize multiple atoms to one “grain” (ball).

This is faster