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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.