[gmx-users] New force fields

David L. Bostick dbostick at physics.unc.edu
Fri May 3 14:51:56 CEST 2002

I agree,

But this is what I was saying.. Gromacs currently allows only one
definition of fudgeQQ while for LJ 1-4s you can just tailor a pairlist to
your own liking.  I understand that 1-4s for every torsion potential is
just a modified version of the potential, but this is how it is done.  If
some guy works for years to get his potential for some molecule to give
reasonable results and for some reason used wierd fudge factors, I would
like to be able to use his potential.  I would rather not go through his
ab-initio calculations and try to fit the dihedrals all over again just so
I can use a globally defined fudge factor.  I guess this is the jist of my


David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	

On Fri, 3 May 2002, David van der Spoel wrote:

> On Thu, 2 May 2002, David L. Bostick wrote:
> >about implementing other forcefields it should be noted that 1-4
> >interactions can be a real headache.  With current gromacs/gromos
> >parameters, it is customary to have no charge-charge fudge factor, but for
> >OPLS 1-4 LJ is
> >scaled by 1/8 and charge-charge interactions are scaled by 1/2 .. or the
> >other way around.  For standard amber (all-atom) it is different.  This
> >becomes hectic if you have molecular species where some things need to be
> >screened and others don't.. i.e. ryckaert bellemans tails on lipids with
> >OPLS parameters, since there is only 1 place to put a fudgeQQ factor in
> >gromacs... or rather, when some species must be screened differently than
> >others.  DL_POLY handles this by placing individual screening factors to be
> >read into the program in the same place that dihedrals are read in.  THis
> >way each dihedral can have a different 1-4 interaction in the system..
> >
> >Currently such problems can be dealt with for LJ interactions by using a
> >simple pairlist and having [pairtypes] tags in the topology files, but for
> >1-4 charge-charge interactions, nothing like this can be dealt with.
> Actually LJ 1-4 is trivial since it is a fixed list. Charge can be given 
> an overall fudge factor now, but one for the whole system (in the defaults 
> section of the top file). On the other hand, having individual charge and 
> LJ factors per dihedral just turns out to be a modified torsion 
> potential, for which one can probably parameterize a cosine expansion. 
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,  	75123 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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