Hi Max, Thanks for the paper. This is helpful. -Dewey Ebert Maximilian wrote: > Hi Dewey, > maybe a little bit off topic but your description of the system reminded me > of a paper I read a couple of years ago. Do you know about the ABF method and > the work of Lamoureux et al? (http://pubs.acs.org/doi/abs/10.1021/ja300129x) > maybe worth checking because it sounds like the simulation you want to > execute (even though they don’t use GROMACS). > Max > On May 31, 2015, at 4:17 PM, MPI <mpi...@gmail.com<mailto:mpi...@gmail.com>> > 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 > 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.
