Thanks, Justin! That's really helpful indeed. You are correct, I want to know what's the energy change in replacing one lipid with the other, hypothesising that going to the "wrong" lipid will imply an energetic cost.
Via umbrella sampling, I would thus: 1) Set up a full system with protein, lipids, solvent, and ions. 2) Pull the protein perpendicularly out of the membrane and into the solvent (which means I'd need a lot of solvent in the direction of the pull, such that there's always enough space to fit the protein and still avoid boundary interactions, as you explain in you tutorial, thanks!). 3) Do the exact same thing with the other system, independently. 4) See just by eye what the difference is and hope it matches my prediction. Now, my question about using umbrella sampling for this purpose: is it reasonable to use the whole membrane (say, the group of lipids) as my immobile reference? In your tutorial you use a chain, in which all members are covalently bound to each other, so I didn't know whether you could use a group of independent molecules instead. I assume it will be fine, then. Thanks again! Best, Victor Sojo -- View this message in context: http://gromacs.5086.x6.nabble.com/Binding-energy-of-membrane-protein-to-the-membrane-lipids-tp5014735p5014742.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
