[gmx-users] Regarding trjconv

Ali Khodayari ali.khodayari at student.kuleuven.be
Sun Dec 2 18:32:12 CET 2018

Thank you Justin.
I tried to define a reference group having the desired orientation and use
-fit. But the box rotates as well. I need to keep the box as it is and just
rotate the solute. Using -fit prompts me to choose the group for least
squares fit and the output, only. When I use -princ in editconf, it orients
the crystal in z direction perfectly. The only problem is that the box
rotates as well, and is not well aligned along the same direction. Any

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Justin
Sent: zondag 2 december 2018 17:38
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Regarding trjconv

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



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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