[gmx-users] to neutralize the system

[Qasim Pars]

Dear gmx users,

I am confused on below questions:

1) Is it necessary to neutralize a protein without ligand?  Does the PME
method work with a charged protein correctly?

2) I have done lots of MD simulations at a charged complex structure
(protein+ligand) with the PME method using GROMACS. I haven't come across
with any problems because of the charge of the system. It means that the
PME method works at a charged complex system properly. In spite of that, do
you think that I need to neutralize a charged complex system?

Can anyone comment on above questions?

Cheers,

-- 
Qasim Pars