In the molecular dynamics study, the interaction distance between the molecule should be 3 angstroms. If it is more than 6 angstrom, is it correct?
Mr. Harun-Ur- Rashid,
Firstly, there is important to clarify your MD methodology?
Secondly, the non-covalent interaction distances are up to 3.45 A (so-called short contacts).
While the distance seems to be a bit large, it is impossible to answer this question without knowing what kind of molecules are we talking about (proteins? other biomolecules? small organic systems?) and how is the distance calculated (the smallest distance between two atoms of molecules?).
Electrostatic interactions can extend well beyond 10 Angstroms (or up to the cut-off, if applied).
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Simulation pertains to the material and efficient causes, i.e., to the application of art of molecular modeling by the artist. Simulation per se is always correct (unless there is a bug in the algorithms). If the simulation does not simulate phenomena correctly, the problem could be: (1) an unskillful use of the molecular modeling tool, (2) an inability of the molecular modeling tool to simulate the form conceived, (3) the form conceived (the questions asked) being wrong (nonsensical).
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