[gmx-users] Placing the molecule in the centre of the box

[Mark Abraham]

> Dear All
>
>  I set up my molecule in the centre of the box using editconf command and
> -c option. Then i solvate the box and run the md step. But after the
> Simulation the molecule doesnot remain anywhere near the centre.

Why should it? You can use options to trjconv to re-center the solute in
the (I assume) periodic box for convenience... but it's irrelevant for the
mathematics, since there's no unique centre of a periodic system.

Mark