[gmx-users] how to keep the ligand inside water box

Justin Lemkul jalemkul at vt.edu
Wed Nov 14 14:48:02 CET 2018

On 11/14/18 7:08 AM, Rahma Dahmani wrote:
> Hi GMX users,
> After running nvt equilibration, my ligand get out the box and before
> proceeding to npt equilibration i want to know how to get (and keep if is
> it possible) the ligand in water box* center* ?

There is no reason to do this. In a periodic (infinite) system, there is 
no such thing as a "center." Your molecule will diffuse, cross periodic 
boundaries, etc. You can recenter after the fact with trjconv, but there 
is no physical need to enforce some visualization convenience.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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


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