[gmx-users] Excluding coulomb interactions only

[David]

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
sure.

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 
> certain.
> 
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-- 
David.
________________________________________________________________________
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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