[gmx-users] system goes out of the water box

[Justin Lemkul]

> Hello all,
>
> I am new to using Gromacs and MD simulation. I am simulating a 9-residue
> drug with a box of water. I generated the box using this:
> editconf -f xx.gro -o xx.gro -d 0.5 -bt cubic
>
> everything seems fine and the MD run went smooth. However when I look at
> the trajectory, I see that the drug goes of the water box and the
> simulation ends up with the drug attached to the outside of the box.
>
> Does this mean that I should increase the size of my box?
> before running the md, the drug was centered into the box of water molecules.
>
> I appreciate any help.
> Thank you
>
> Belquis Mothana

There are a number of threads in the mailing list archive about this.  A fairly
recent one can be found at:

http://www.gromacs.org/pipermail/gmx-users/2007-February/025797.html

I believe that deals with a similar problem, based on what you've described.  If
you're applying periodic boundary conditions (pbc = xyz) in your .mdp file, then
there shouldn't be anything wrong with the simulation.  Search the archives for
more information.

Best of luck,
Justin