Hi Tsjerk, Thank you so much for being so patient! I have yet another question. The membrane I got from the Martini website already has water in it. Do I need to add more water and if so why?
Also how exactly do I use trjconv to put all molecules in the box? Sorry for being so annoying need a lot of elaboration! Tsjerk Wassenaar wrote > 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 < > nshafique@ > > 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 > gmx-users@ >> 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-request@ > . >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > gmx-users mailing list > gmx-users@ > 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-request@ > . > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/Creating-a-monolayer-from-Martini-bilayer-tp5008740p5008751.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-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