Practical simulation methods
Molecular dynamics simulations in biochemistry

The system's initial coordinates can have different origins:

• (i) macromolecule structures determined by NMR or X-ray crystallography ;

• (ii) construction of atomic coordinates using computer graphics software and values for bond lengths and angles (in silico construction);

• (iii) structures predicted by bioinformatics.

Case (i) represents the situation of choice for starting a simulation, as it can be based on experimental structural information. System coordinates can often be downloaded...