Hi Neha, You can use trjconv with option -pbc mol to put all molecules in the box. If you want a vacuum, you probably don't want to add more water. But just play with it and see what comes out. CG simulations are fast enough for that kind of trial-and-error.
Cheers, Tsjerk On Mon, Jun 3, 2013 at 8:26 PM, Neha <[email protected]> wrote: > 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 [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
