Note that the solution Dallas suggested will work (along with changing the resulting box dimensions), but that it may lead to clashes at periodic boundaries. You may need to re-minimize (perhaps with soft-core potentials if there are serious clashes) and re-equilibrate, which would probably defeat the purpose of starting from a pre-equilibrated structure. It's a lot easier to duplicate a bilayer than it is to shrink it.
Consider using a server/tool to generate a system for you instead, such as the CHARMM-GUI. Kevin On Thu, Aug 8, 2019 at 8:00 PM Dallas Warren <dallas.war...@monash.edu> wrote: > Select molecules within the appropriate x y coordinates (if that is the > plane that the membrane is in) that will provide that number of molecules, > > https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmanual.gromacs.org%2Fcurrent%2Fonlinehelp%2Fselections.html&data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cfc230b2d27d640e458d208d71c75b0a5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637009164119064029&sdata=FT9iErLytB6N7jLMlEa0ITbjb2OJkKCQ6sv1HN9kZRQ%3D&reserved=0 > > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On Fri, 9 Aug 2019 at 02:57, Pradeepa Kumari <pradeepakumar...@gmail.com> > wrote: > > > I want to extract 128 DPPC bilayer section(1/4) from pre-equilibrdated > 512 > > DPPC bilayer.How can I do this with gromacs 5.1.4? Any assistance you can > > provide would be greatly appreciated. > > > > Thanking you in advance. > > > > Regards, > > dananjana > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > > https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cfc230b2d27d640e458d208d71c75b0a5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637009164119074020&sdata=PCpZVGKfHLK34rFBtC6rAXGL9FejBS27oniAFOyQwns%3D&reserved=0 > before > > posting! > > > > * Can't post? Read > https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cfc230b2d27d640e458d208d71c75b0a5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637009164119074020&sdata=fypET%2B%2Fwkd1JXAIL47QLiZY55RPttfHYDd5mOdmz58M%3D&reserved=0 > > > > * For (un)subscribe requests visit > > > https://nam01.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%7Cfc230b2d27d640e458d208d71c75b0a5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637009164119074020&sdata=bJ%2F%2FEO2wm%2FCt%2F%2FMqlvwst4Qi0wJXuGv%2BhT0bqrHqXW4%3D&reserved=0 > or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_List&data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cfc230b2d27d640e458d208d71c75b0a5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637009164119074020&sdata=PCpZVGKfHLK34rFBtC6rAXGL9FejBS27oniAFOyQwns%3D&reserved=0 > before posting! > > * Can't post? Read > https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists&data=02%7C01%7Ckevin.boyd%40uconn.edu%7Cfc230b2d27d640e458d208d71c75b0a5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637009164119074020&sdata=fypET%2B%2Fwkd1JXAIL47QLiZY55RPttfHYDd5mOdmz58M%3D&reserved=0 > > * For (un)subscribe requests visit > > https://nam01.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%7Cfc230b2d27d640e458d208d71c75b0a5%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637009164119074020&sdata=bJ%2F%2FEO2wm%2FCt%2F%2FMqlvwst4Qi0wJXuGv%2BhT0bqrHqXW4%3D&reserved=0 > 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.
