Hi, Depends on what kind of restraint you are trying to apply. If you're just trying to restrain head groups during the initial equilibration period, you can feed -r your actual structure, since the restraints should be relative to current positions.
If instead you're following the pore-forming protocol used to equilibrate between leaflets, then the tail coordinates are just set to the center of the vesicle. They're used for cylindrical flat-bottom potentials in this case, which project out along the x, y, and z axis and repel the tails from those cylinders. Shameless plug for a tool developed in our lab that takes a more quantitative approach to estimating interleaflet area distances so that you can avoid a length pore-based equilibration. https://github.com/MayLab-UConn/BUMPy Kevin On Tue, Oct 30, 2018 at 5:40 AM, Francis Coleman <[email protected]> wrote: > Hi, > > I've been using CHARMM-GUI in an attempt to form coarse-grain vesicles but > things aren't working out for one system. Before I start changing anything, > I was wondering how the position restraint file for the lipid tails i.e. > lipidtail_posres.pdb was generated. Or more generally, what is the command > to generate a position restraint file that can be read by grompp with the > '-r' option? In the past, I've only applied restraints to proteins and it > was clear what commands I required. > > Thanks. > > > Sent from Outlook<https://na01.safelinks.protection.outlook. > com/?url=http%3A%2F%2Faka.ms%2Fweboutlook&data=02%7C01% > 7Ckevin.boyd%40uconn.edu%7C0d2bc0da508e43b2ebbe08d63e4bb6d3% > 7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636764892263951746&sdata= > SYisgDFf4TQP4LgX0pRpcKaKkvK62Ai5iwZylFQ9uhg%3D&reserved=0> > -- > Gromacs Users mailing list > > * Please search the archive at https://na01.safelinks. > protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org% > 2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02% > 7C01%7Ckevin.boyd%40uconn.edu%7C0d2bc0da508e43b2ebbe08d63e4bb6d3% > 7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636764892263951746&sdata= > XKmimnCD0yTxF8t4bgEJkURzqjOTlVMIUNIbbpoPP0s%3D&reserved=0 before > posting! > > * Can't post? Read https://na01.safelinks.protection.outlook.com/?url= > http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists& > data=02%7C01%7Ckevin.boyd%40uconn.edu%7C0d2bc0da508e43b2ebbe08d63e4bb6d3% > 7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636764892263951746&sdata= > mHV6IEsYFMp7dKOz0piYdjlZ%2FywutFHNJPhIUF9OsJ8%3D&reserved=0 > > * For (un)subscribe requests visit > https://na01.safelinks.protection.outlook.com/?url= > https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo% > 2Fgromacs.org_gmx-users&data=02%7C01%7Ckevin.boyd%40uconn.edu% > 7C0d2bc0da508e43b2ebbe08d63e4bb6d3%7C17f1a87e2a254eaab9df9d439034 > b080%7C0%7C0%7C636764892263951746&sdata=fZQ159Hp5yiqoHeM1T9zYd0sphJOby > DwrQlVVc8g7Ps%3D&reserved=0 or send a mail to > [email protected]. > -- 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 [email protected].
