[gmx-users] Questions about free energy calculation tutorial

[gozde ergin]

Thank Justin, ok I understand now. 
Then I need to run the simulation with +1 charge, since I made 0 of all the charges in SDS, Na+ charge will stay there.
Do you think it is ok run with +1 charge?

> On 04 Nov 2016, at 13:36, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> No, you should not.  The topology you posted before had Na+ as part of the SDS [moleculetype] and you were decoupling the whole thing.  This is what I am saying you should not be doing if you're trying to get just the hydration free energy of SDS.
> 
> -Justin