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

Erik Marklund erik.marklund at kemi.uu.se
Thu Sep 8 11:42:03 CEST 2016

Dear George,

Is this not just a visualisation issue because of periodic boundary conditions? Are you sure that the vacuum was not present in the input coordinate file?

Kind regards,

> On 7 Sep 2016, at 23:58, George Pantelopulos <gpantelopulos at gmail.com> wrote:
> 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
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