[gmx-users] Regarding trjconv

Justin Lemkul jalemkul at vt.edu
Sun Dec 2 17:37:42 CET 2018

On 12/2/18 11:22 AM, Ali Khodayari wrote:
> Dear all,
> I am trying to re-center and re-orient an md resulted solute in a box. Yet,
> I need the box to hold its position and I only need a group of atoms to
> align along z-direction. Trjconv centers the group in the box but the
> desired sub-group has a slight inclination which is needed to be oriented
> along z axis. Is there any particular trick to do this? Maybe in combination
> with editconf?

trjconv -fit with a suitable index group that defines the orientation 
you want.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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