Hi Neha, A single structure is like a trajectory with only one frame :p trjconv works on those as well. Right, set the center at 0,0,0 and choose the lipids as group for centering.
Cheers, Tsjerk On Mon, Jun 3, 2013 at 7:31 PM, Neha <[email protected]> wrote: > Hi, thank you so much! > > This way seems promising, however I am not sure how to center the bilayer > around z=0. I thought I could use editconf but I might be confused as to > how > Gromacs centers its objects. If I put -center 0 0 0 does that mean the > bilayer is centered around z = 0? > > Also I thought that trjconv only dealt with trajectory files. What I have > right now is a structure file, a topology file and an map file. After I > have > solvated, I will still only have a new structure file, so what would the > trjconv be acting on? > > Thank you so much for helping out a newbie! > > > Hey :) > > Just center the bilayer around z=0, solvate and put all molecules in the > box with trjconv. Then add 10 to the PBC Z-component (third number from the > last line in the .gro file). > > Cheers, > > Tsjerk > > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740p5008747.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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. -- 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
