Firefly and PC GAMESS-related discussion club

Learn how to ask questions correctly

Pedro Silva
pedros@ufp.edu.pt

means: add bonds between atoms 1 and 9, 2 and 9, 3 and 9, 4 and 9, 1 and 15, 3 and 15, 4 and 15

"is it necessary that we connect the all adsorbate atoms to the surface ?"

No. Usually a few will be enough

"which atoms should be connected to the surface by NONVDW ?"

I would choose three or 4 atoms (not very close to each other)

"Does FF optimize the bonds that were not prepared by NONVDW ? "

The NONVDW bonds are also optimized. ALL bonds not frozen ezplicitly in ifzmat are optimized.