[gmx-users] to neutralize the system

[Tsjerk Wassenaar]

Hi Qasim,

Not only should you neutralize the system, but you should add additional
ions too. The behaviour of charged side chains which can find a partner ion
from solution is different from those that can't. You won't see any
problems, but the results will be affected. Not coming across any problems
is not good quality assurance in simulations.

Cheers,

Tsjerk
On Jun 15, 2016 00:01, "Qasim Pars" <qasimpars at gmail.com> wrote:

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
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