[gmx-users] vaccume simulation

[tasneem kausar]

Dear gmx-users
I am trying to calculate rmsd for protein backbone. I have done simulation
in vacuum. There are for negative charges in the system. During solvation
via genbox, 4 water molecule were added using -maxsol. The charges have
been neutralized by addition of 4 Na ion and water molecules were replaced
by these ions. Then after minimization I have run full md for 50 ns.

if there is any other way to neutralize the charge in vacuum, please tell.
Is the way I have opted for vavuum simulation right?

Any kind of help will be appreciated.

Thanks and Regards