[gmx-users] Dihedrals/Impropers

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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