[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

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!

[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

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