[gmx-users] Coordinate File and Origin in Gromacs // Separating Bilayer Leaflets

Justin Lemkul jalemkul at vt.edu
Thu Sep 25 19:35:56 CEST 2014

On 9/25/14 12:38 PM, Neha Shafique wrote:
> Hi everybody,
> I am running Gromacs 4.6, and simulating a Martini bilayer. For some of the
> analysis, I want to separate the bilayer into leaflets and analyze their
> data individually. I was wondering if Gromacs had a script or tool that
> would allow me to do that.

You can consider any group of atoms you like by creating a suitable index group. 
  The tools are make_ndx and g_select, depending upon how complex the selections 
are.  For individual leaflets, it is simple to use either tool.

> If there is no pre-existing tool, I would need to write a script myself.
> However, I realized that I don't know how Gromacs prints out coordinates in
> the trajectory. I read the .trr files, and it didn't really say very much.
> Is the origin in the 'middle' of the box, is it in a corner? Can I change
> the convention? Please let me know if you have any suggestions!

The corner of the box is set at the coordinate origin and built outward in the 
positive x, y, and z dimensions.  If you want to change the position, that is 
what trjconv -trans is for.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list