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

MPI mpi566 at gmail.com
Sun May 31 22:17:11 CEST 2015

 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


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 ?


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