[gmx-users] 1-4 non-bonded
David van der Spoel
spoel at xray.bmc.uu.se
Mon Jan 19 14:13:01 CET 2004
On Mon, 2004-01-19 at 13:34, 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
> 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
> different scaling factors (if at all) for these interactions as
> compared to
> regular, 1-5 or higher ineteractions? (For example, AMBER does it.)
yes there are 1-4 interaction. there are no scaling factors, but in many
cases the repulsion term is reduced. these are listed in your topology
under pairs. see also chap. 4 of the manual.
> Thanks, Peter Nagy
> University of Toledo
> pnagy at utnet.utoledo.edu
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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