t.piggot at soton.ac.uk
Thu Jun 21 17:23:10 CEST 2018
Further to Justin's comment, it is worth explicitly stressing that
unlike most other force fields, GROMOS force fields do not typically
include every proper dihedral. Rather they only have one dihedral across
the same two central atoms (bar multiple dihedrals applied to the same
four atoms). There are exceptions to this, such as in sugars.
On 21/06/18 15:24, Justin Lemkul wrote:
> 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
Dr Thomas Piggot
University of Southampton, UK.
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