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Re: BAD DELOCALIZED COORDINATES

Pedro Silva
pedros@ufp.edu.pt


Adding extra coordinates with NONVDW has no effect on the pysics of the process, but it helps FF build appropriate delocalized coordinates.
It works like this: assuming you have a surface with 8 atoms (numbered 1 through 8) and that the atom you want to adsorb a benzene (12 atoms, numbered 9 therough 20), you may build new non-physical bonds with:

NONVDW(1)=1,9,2,9,3,9,4,9,1,15,2,15,3,15,4,15

FF then takes the original bonds it could find (e.g. between 1 and, 1 and 4. etc...), adds the new bonds, computes all possible angles and dihedrals defined by ALL bonds, and builds DLCs with these coordinates.


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