[gmx-users] Excluding coulomb interactions only
spoel at xray.bmc.uu.se
Sat Nov 20 09:28:12 CET 2004
On Fri, 2004-11-19 at 15:40 -0700, Walter Ash wrote:
> What is the behavior of gromacs if you are excluding 1-4 interactions,
> but have pairs of atoms with L-J parameters listed under [ pairtypes ]?
he interactions ARE calculated.
> Is it possible to exclude only 1-4 coulomb interactions while
> maintaining interactions defined in [ pairtypes ]? Also, does the LJ
> fudge factor (e.g. the OPLS-AA 0.5 factor) get applied to the
> interaction parameters listed in [ pairtypes ] or is this factor only
> used when regular LJ parameters from [ atomtypes ] are used (with
> combination rules, if needed)?
You could probably exclude 1-4 Coulomb by setting the constant fudgeQQ
in e.g. ffoplsaa.itp 0. If you do that to a protein it will blow up Iäm
The fudgeLJ factor is used in generating the pair parameters from the
normal parameters, the fudgeQQ is passed to mdrun in the tpr file.
> I've seen some stuff in the archives but I couldn't find anything very
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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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