Discussion:
[gmx-users] Regarding trjconv
Ali Khodayari
2018-12-02 16:22:00 UTC
Permalink
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?



Best,

Ali
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Justin Lemkul
2018-12-02 16:37:30 UTC
Permalink
Post by Ali Khodayari
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
--
==================================================

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

***@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================
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Ali Khodayari
2018-12-02 17:32:05 UTC
Permalink
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
suggestions?
Best,
Ali


-----Original Message-----
From: gromacs.org_gmx-users-***@maillist.sys.kth.se
<gromacs.org_gmx-users-***@maillist.sys.kth.se> On Behalf Of Justin
Lemkul
Sent: zondag 2 december 2018 17:38
To: gmx-***@gromacs.org
Subject: Re: [gmx-users] Regarding trjconv
Post by Ali Khodayari
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

--
==================================================

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

***@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================

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mail to gmx-users-***@gromacs.org.
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