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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Sep 8 08:20:32 CEST 2016

Hi George,

How did you build the starting structure?

The quadrants are due to distribution over cores/nodes. You can try EM on a
single core for a few steps, but it seems that the system is too stretched
anyway, so I think that won't really solve your problem.



On Sep 7, 2016 11:58 PM, "George Pantelopulos" <gpantelopulos at gmail.com>

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
Thank you for the help,
George Pantelopulos
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