Hi Ariel, If it works, it's good :) It really only affects the visualization... It doesn't change the system.
Cheers, Tsjerk On Tue, Feb 21, 2012 at 10:33 AM, Siew Wen Leong <[email protected]> wrote: > Dear all, > > Have anyone tried using CHARMM36 equilibrated POPE bilayer by Dr.Klauda > http://terpconnect.umd.edu/~jbklauda/research/download.html? > > I am planning to use the membrane patch for a transmembrane protein > simulation. At first visualization, the membrane patch consists of a bilayer > with a single layer of water and then several lipids sticking out from the > opposite side of the water. So I presumed that to be an effect of PBC. > > How can I correct this in Gromacs? > > I've generated a .tpr for the system to use trjconv to manipulate the PBC > box. > > Out of all the combinations of pbc treatments, this one works: > > trjconv -f pope80-c36box.gro -o pope80_pbc10.gro -s pope80.tpr -pbc mol > > This puts the center of mass of the molecules in the box so I got a lipid > bilayer with a single, thick layer of water. > then followed by > > trjconv -f pope80_pbc10.gro -o pope80_pbc11.gro -s pope80.tpr -pbc mol > -center > > to center the membrane on POPE. > > The result looks fine (a hydrated bilayer) but I'm a new user to Gromacs so > I just wanted to ask if the workflow is reasonable. > > -- > Regards, > Ariel. > > > -- > gmx-users mailing list [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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list [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
