[gmx-users] Adding a substrate into protein-lipid bilayer system

[MPI]

 Dear Users,

    I have a protein-lipid bilayer system and this protein is an ion
channel.  I would like to force a substrate eg, ammonia (NH3) passing
through this channel.

I wonder when it is appropriate to add NH3 into the system and how to
setup the control of temperature coupling in thermostats.
For example,

1.  add NH3 first with the protein and  then embed protein-NH3  into the lipid

or

2.  embed the protein into  lipid with an equilibration,  followed by
adding NH3 into the system


Also,  if the substrate has a charge, which order is preferred ?


Thanks,
Dewey