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

[Justin Lemkul]

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

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

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