btw: you forgot to copy the mailing list again.
any future replies that will only go to myself
will either be ignored, or you have to hire me
as a personal consultant. i only give "free" advice
if it is in the public so that it is publicly accessible
through the mailing list archives and others can
contribute to the discussion as the see fit. thanks.
Thank you for your reply Axel.It is very helpful for me.
Keeping in mind your advices I will meditate about my problem.
So hybrid simulation with EAM is a complex way and as you said I don't
need such a level of detail in my work.However I don't want to fix
gold atoms and Au-S bonds.I will search for an easier description that
will be more compatible with CHARMM.For now I found this work :
Heinz, H.; Vaia, R. A.; Farmer, B. L.; Naik, R. R. J. Phys. Chem. C
2008, 112, 17281–17290.
This approach appears to be better in my situation.
since you didn't tell what you want to learn from your
simulation, it is difficult to give any advice. however,
your reasoning and resulting choice doesn't seem
conclusive to me. if you want Au-S-C properly represented
at this point in time, i don't think there is an alternative
to using a quantum chemical, or at least an approximate
quantum chemical method (like DFTB) with a lot of luck.
the only justification for a mechanical coupling is that
you would be doing a simulation, where only the
gold structure would matter and it would be deformed
by some force pulling or pushing the molecules attached
so what is it in your simulation project that would need
the gold atoms to be moving?
also, if you cannot ignore the detail of the gold structure
to be rigid, why can you ignore the (IMO larger) issue of
not representing the Au-S-C interactions well?