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

Neha nshafique at wesleyan.edu
Mon Jun 3 19:31:49 CEST 2013

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).



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.

More information about the gromacs.org_gmx-users mailing list