3. Practical simulation methods
The aim is to analyze a molecular dynamics trajectory and make the link with the experiment.
3.1 Choice of initial coordinates
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...
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Practical simulation methods
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