jalemkul at vt.edu
Thu Jun 21 16:25:08 CEST 2018
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.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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