Hello,
I am learning how to perform QM/MM
calculations using Gromacs and Orca. I have already managed to run a calculation
from a simple tutorial, but I have some doubts (not all of them specific to the
Gromacs/Orca duo), and I hope someone more knowledgeable than I can help
me.
1) As far as I can tell, Orca only takes vdW
interactions into account (via LJ parameters of the force fields) if
a full QM/MM optimization is performed for each MD step - the LJ parameter files
only appear if the option for a full geometry otimization of the QM part is set.
Is there any way to make Orca take the LJ parameters into account if a
single-point calculation is performed?
2) If there is
no way to do it just by setting flags in Gromacs, is there some way to go around
this? Some effective way of making he QM and MM regions be taken into account
when calculating the total energy of the QM + MM
system?
3) Now a more fundamental question, not exactly
related to Gromacs or Orca, but to QM/MM itself. In which situations (in a
general way) would the neglect of LJ interactions between the two sub-regions be
acceptable, and which would be not?
Best
regards,
---
Dr. Marcos Verissimo Alves
Prof.
Adjunto II, Curso de Física Computacional
Instituto de Ciências
Exatas
Universidade Federal Fluminense
Volta
Redonda - RJ, Brasil