[gmx-users] 1-4 non-bonded
lindahl at csb.stanford.edu
Mon Jan 19 14:19:00 CET 2004
Gromacs is pretty flexible when it comes to 1,4 interactions. You can
scale coulomb and/or L-J with a fixed factor for all interactions, or
you can assign separate 1,4 interaction parameters for each pair of
Check out the force field files that are included with Gromacs for
examples. OPLS-AA/L uses fixed scaling factors, while Gromos96 uses
explicit separate 1,4 parameters.
On Jan 19, 2004, at 1:34 PM, Nagy, Peter I. wrote:
> Dear GROMACS Users,
> Some force fields (AMBER, Tripos/Sybyl) considers 1-4 VdW and
> electrostatic interactions.
> The GROMACS manual says that the non-bonded interactionas are based
> on a neighbor list, in which exclusions are alrady removed.
> The bonded interactions are based on a fixed list of atoms. They
> 4-body, dihedral angle interactions.
> Does combination of the two definitions mean that GROMACS does not
> consider 1-4 VdW and electrostatics? If it still does, does GROMACS use
> different scaling factors (if at all) for these interactions as
> compared to
> regular, 1-5 or higher ineteractions? (For example, AMBER does it.)
> Thanks, Peter Nagy
> University of Toledo
> pnagy at utnet.utoledo.edu
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