[gmx-users] Scaling non-bonded interactions

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 18 08:51:30 CET 2005

On Thu, 2005-03-17 at 15:41 -0600, Glenn Johnson wrote:
> Is there some way to scale 1,5 and 1,6 non-bonded interactions during a
> calculation with Gromacs?
Not trivial, you can take these out of the nonbonded list by setting
nrexcl to 5 or 6 in the topology. But then you have to modify code to
gerate these as pairs. As it works now you will have to scale the
nonbonded for all pairs (1-4 and in your case 1-5 and 1-6) in the same
manner. If that's fine with you you'd have to edit some code in grompp
to generate not only 1-4 but also 1-5/6 lists.
> Thanks.
David van der Spoel, PhD, Assoc. 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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