[gmx-users] centering with trjconv

Justin Lemkul jalemkul at vt.edu
Tue Aug 26 20:12:27 CEST 2014

On 8/26/14, 12:30 PM, Eric Smoll wrote:
> Hello GROMACS users,
> I have created an infinite liquid film system by building a slab of
> molecules in a 3D periodic unit cell where two dimensions of the film (x
> and y) extend out to the edge of the unit cell and one (z) does not.
> I found the slab drifts along the z-dimension during MD and I am trying to
> post-process the trajectories to anchor the slab in the center of the unit
> cell.
> "trjconv -pbc mol -center -boxcenter" works well for most trajectories
> *unless* the slab drifts so much that it comes in contact with the z
> boundary. When this occurs,  "trjconv -pbc mol -center -boxcenter" anchors
> it in a different location. Any ideas how I can anchor the system to the
> center of  the unit cell in this situation?

The -fit options should help here, either progressive or translation.



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


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