Editing Molecular modelling (section)

===Coordinate representations===
Most force fields are distance-dependent, making the most convenient expression for these Cartesian coordinates.  Yet the comparatively rigid nature of bonds which occur between specific atoms, and in essence, defines what is meant by the designation ''molecule'', make an internal coordinate system the most logical representation.  In some fields the IC representation (bond length, angle between bonds, and twist angle of the bond as shown in the figure) is termed the [[Z-matrix (chemistry)|Z-matrix]] or torsion angle representation. Unfortunately, continuous motions in Cartesian space often require discontinuous angular branches in internal coordinates, making it relatively hard to work with force fields in the internal coordinate representation, and conversely a simple displacement of an atom in Cartesian space may not be a straight line trajectory due to the prohibitions of the interconnected bonds.  Thus, it is very common for computational optimizing programs to flip back and forth between representations during their iterations. This can dominate the calculation time of the potential itself and in long chain molecules introduce cumulative numerical inaccuracy. While all conversion algorithms produce mathematically identical results, they differ in speed and numerical accuracy.<ref name="Parsons_2005" />  Currently, the fastest and most accurate torsion to Cartesian conversion is the Natural Extension Reference Frame (NERF) method.<ref name="Parsons_2005">{{cite journal | vauthors = Parsons J, Holmes JB, Rojas JM, Tsai J, Strauss CE | title = Practical conversion from torsion space to Cartesian space for in silico protein synthesis | journal = Journal of Computational Chemistry | volume = 26 | issue = 10 | pages = 1063–8 | date = July 2005 | pmid = 15898109 | doi = 10.1002/jcc.20237 | s2cid = 2279574 }}</ref>