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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jun 3 19:55:41 CEST 2013

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.



On Mon, Jun 3, 2013 at 7:31 PM, Neha <nshafique at 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
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Tsjerk A. Wassenaar, Ph.D.

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