[gmx-users] Re: Creating a monolayer from Martini bilayer
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 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] Re: Creating a monolayer from Martini bilayer
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 nshafi...@wesleyan.edu 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 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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] Re: Creating a monolayer from Martini bilayer
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 lt; nshafique@ gt; 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 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] Re: Creating a monolayer from Martini bilayer
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 nshafi...@wesleyan.edu 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 lt; nshafique@ gt; 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 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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
