[gmx-users] Large (600k particle) semi-isotropic lipid bilayer system transformed into vacuum-separated coordinates by grompp and mdrun

[George Pantelopulos]

Dear all,

I have been trying to equilibrate a very large lipid bilayer system for the
past few days, but I have not been able to move past a very curious error
that happens when producing a tpr file and running miminization or MD.

The system ends up being split in to 8 quadrants, leaving sizeable vacuums
between each quadrant, and the coordinates of the system are transposed.
I've tried to resolve this via various combinations of minimization and
equilibration schemes but have had no success. At this point, I think I may
only turn to the mailing list for advice.

Does anyone have an idea of what might be going on and how I could resolve
this?
Thank you for the help,
George Pantelopulos