[gmx-users] Re: Creating a monolayer from Martini bilayer

[Neha]

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





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