On 5/31/15 4:17 PM, MPI wrote:
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
If you want NH3 to pass through the channel, I'd say (2), more or less, but really you should add NH3 as a cosolvent as part of the equilibration. Add the NH3 in the box, add water, and equilibrate.
Also, if the substrate has a charge, which order is preferred ?
Charge shouldn't affect the protocol. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.