Hi, Justin's tutorial is not a fully generalized procedure for umbrella sampling; it shows a workflow for one specific example which is not always applicable to other systems.
In general, you don't have to use position restraints for anything in umbrella sampling. Justin uses them to keep the fibril in place for specific reasons, as noted in the paper he based the tutorial on. That said, what are you trying to do? Adding restraints to the bilayer is probably a bad idea, seeing as how the motion of the bilayer is an important physical behavior. Are you calculating the PMF for a molecule traversing a lipid bilayer? If so, there are many examples in the literature that detail a procedure that's probably much more relevant to you. Best, John > Dear GMX users, > > I would like to ask about position restraint during the umbrella sampling. > 1. Is it need to make position restraint of lipid bilayer during the > umbrella sampling simulation? > 2. The position restraint was used for the B chain of amyloid-beta > peptides > in prof. Justin's tutorial. Can I run the simulations without position > restrain of lipid molecules in the case of lipid bilayer? > or > 3. Can I use the position restraint for only phosphorus atoms of the > headgroups of both leaflets? > > If you have any experience, please let me advise which one is better for > this kind of calculation. > > Best regards, > > Mijiddorj > -- > 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. > -- 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.