[gmx-users] centering with trjconv

Eric Smoll ericsmoll at gmail.com
Tue Aug 26 18:30:53 CEST 2014

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

"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?


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