[gmx-users] 1-4 non-bonded

Nagy, Peter I. PNAGY at UTNet.UToledo.Edu
Mon Jan 19 13:35:01 CET 2004

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 include
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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