On 6/21/18 10:22 AM, Salman Zarrini wrote:
Dear all, I wonder if it is necessary to list all the Dihedrals/Impropers of the molecule in a MD simulation? If not so, what kind of Dihedrals we don't need to list?
The topology needs to contain every interaction that's relevant. Nothing is implicit or assumed. Most existing functional forms have dihedrals on every torsion, although sometimes they have force constants set to zero so that topological integrity can easily be checked. The use of impropers depends on the force field and its convention.
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