[gmx-users] Neutral simulation box

[Deepa Rajamani]

I am running a simulation on protein. I have
the following questions.

1. Should I be neutralizing the simulation box if I use the PME for
calculating long range electrostatics.

2. IF I do will the mobility of the charged side chains be affected by the
counter ions added.

3. IF yes for my second question, how do I overcome this problem.

Thanks in advance.

Deepa