Re: [gmx-users] Creating a monolayer from Martini bilayer
You could try packmol or the MembraneEditor. http://www.cellmicrocosmos.org/index_cm2.php Dipl.-Inf. Gunther Lukat g.lu...@gmx.net www.aplvoro.org Am 03.06.2013 um 18:43 schrieb Neha : > Hello everybody, > > I am a new user to Gromacs and am working on lipid simulations with the > Martini forcefield. The Martini website provides a pre-equilibrated DPPC > bilayer, and I was wondering if there were any told that would allow me to > convert this bilayer into a monolayer. For periodic boundary conditions to > work, I was thinking of a stack that would go like > > Water > Lipid Heads > Tails > Vacuum > Tails > Lipid Heads > Water > > Is there any way to split apart the provided bilayer using some combination > of Gromacs tools and introduce a space of at least 10 nm which is apparently > the distance needed for the tails to not interact with each other? > > If there is no way of simply splitting the bilayer, what would you recommend > for creating a simulation of lipid monolayers from a single DPPC molecule? I > feel like I could use genconf but it might require too much equilibration. I > am hopeful that there is some way of simply working with the provided > bilayer. > > Any help would be appreciated! > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing listgmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] T-Coupling groups in NVT
I general, I have good results with coupling Ions together with the water. Dipl.-Inf. Gunther Lukat g.lu...@gmx.net www.aplvoro.org Am 21.03.2013 um 13:56 schrieb Shima Arasteh : > Hi, > > I am simulating a system of POPC/Water/Ions/protein. > Ions are 1 M NaCL and 3 CL atoms to neutralize the system. > > In NVT step, I have coupling groups as : > tc-grps= Protein POPCSOL_CL > > comm_grps= Protein_POPC SOL_CL > > when I run the grompp for NVT, I get the error that the 615 Na atoms are not > part of any of the T-Coupling groups. > > Now, I 'd like to know if I need to couple Na with SOL_CL such as SOL_CL-Na ? > Or I need to create a seperate group for Na? > > Would you please give me suggestions? > Thanks in advance. > > > Sincerely, > Shima > -- > gmx-users mailing listgmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
