>From: Mark Abraham <mark.j.abra...@gmail.com>
>To: gmx-us...@gromacs.org, "gromacs.org_gmx-users@maillist.sys.kth.se"
> <gromacs.org_gmx-users@maillist.sys.kth.se>
>Subject: Re: [gmx-users] Segmentation Fault - Water on Substrate
>Message-ID:
>
Hi,
You're presumably making one of your formerly periodic dimensions
differently periodic when you combine your boxes. If your input structure
has molecules with coordinates that are broken across the former boundary,
you need to make them whole before your merge can work sanely.
Mark
On Sun,
Dear Gromacs users,
I am want to simulate water on a substrate.
I have a water.pdb file with the coordinates of a cuboid of water and a
substrate.pdb file with the coordinates of the substrate. The box dimensions
along the x and y directions are identical for both files.
I run two simulations
