[gmx-users] Adding water

[Bob Johnson]

Hi,
I'm not doing anything to the box size when I add water molecules. Also, my
system is in vacuo and at constant volume. Thus, when I add a water molecule, I
place it in empty space. Therefore, the system shouldn't be in an energetically
unfavorable configuration upon adding just a single water molecule.

It seems to me that there is something wrong going on with the LJ interactions.
Although I'm using gen-pairs, the only molecule that has a pair list in its
topology file is the DNA. When simulating ONLY the DNA molecule, it is stable
even if I remove the pair list in the topology file. However, when I combine
the nanotube, DNA, and water, the simulation crashes unless the DNA pair list
is present. Does this have anything to do with it?
Thanks,
Bob