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

bmmothan at ucalgary.ca bmmothan at ucalgary.ca
Tue Apr 24 23:53:10 CEST 2007

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

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