[gmx-users] New force fields

David van der Spoel spoel at xray.bmc.uu.se
Fri May 3 11:53:04 CEST 2002

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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