Re: [gmx-users] How to construct mixed lipid bilayer
Let me correct myself :). Its pre-equilibrated. Not pretty equilibrated. :) On Nov 13, 2013 7:23 PM, "Arun kumar V" wrote: > Start with packmol if you want to start from scratch. Or else get a pretty > equilibrated mixed lipid bilayer if available somewhere on web. > On Nov 13, 2013 6:45 PM, "Nikhil Agrawal" wrote: > >> Dear All, >> >> can anyone tell me how to construct mixed lipid bilayer in gromacs >> >> id possible also provide me the command to construct the mixed bilayer >> >> >> Thanks in advance >> >> Nikhil >> -- >> -- >> gmx-users mailing [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- gmx-users mailing [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to construct mixed lipid bilayer
Hi Nikhil, The first step would be to determine what forcefield you are going to use for the lipids. If you are going to use Charmm or Slipids, you can use charmmgui (just google it). If you are planning to use the Gromos forcefields, you can check Prof. Tieleman's website or lipidbook for pure bilayers and then build your own from scratch using packmol... Hope this helps... On Wed, Nov 13, 2013 at 6:44 PM, Nikhil Agrawal wrote: > Dear All, > > can anyone tell me how to construct mixed lipid bilayer in gromacs > > id possible also provide me the command to construct the mixed bilayer > > > Thanks in advance > > Nikhil > -- > -- > gmx-users mailing [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to construct mixed lipid bilayer
Start with packmol if you want to start from scratch. Or else get a pretty equilibrated mixed lipid bilayer if available somewhere on web. On Nov 13, 2013 6:45 PM, "Nikhil Agrawal" wrote: > Dear All, > > can anyone tell me how to construct mixed lipid bilayer in gromacs > > id possible also provide me the command to construct the mixed bilayer > > > Thanks in advance > > Nikhil > -- > -- > gmx-users mailing [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
