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

Mark Abraham mark.abraham at anu.edu.au
Tue Jan 9 08:20:06 CET 2007

> 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.


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