[gmx-users] about complex MD

[Natapol Pornputtapong]

Now I work on protein-ligand complex by GROMACS. The system that I
prepare,has a ligand on outer of cell. When I run dynamics the ligand
cannot soak in to the water and don't react with protein molecule. This
is the first problem.
>From past, I change the ligand coordinate to put the ligand into waters
but when I run dynamics on this system the ligand is kicked from the
system. What can I do for these problems. Please suggest me.

Thank you very much
Natapol Pornputtapong