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

[Tsjerk Wassenaar]

Hi George,

Oh, quadrants over PBC, so it just completely ruptured. It means the area
per lipid is really off in your starting structure. Where did you get it
from?

Cheers,

Tsjerk

On Sep 8, 2016 3:54 PM, "George Pantelopulos" <gpantelopulos at gmail.com>
wrote:

> Dear Tsjerk and Erik,
>
> Thank you for the responses!
>
> The initial structure is a complete bilayer with no vacuum in a rectangular
> box.
>
> 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.
>
>
> I had thought this as well, at first, but even running on a single
> processor for one step produces this problem -- it is for this reason that
> I think it has something to do with how GROMACS is interpreting the system.
>
> 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?
>
>
> I am sure that there was no vacuum present in the input coordinate file. I
> had thought that it might be a bizarre visualization issue, but after a
> very rigorous minimization and annealing from 0K, the system not only
> remains split into quadrants, but the edges of each quadrant deform from
> squares into more smoothly curved shapes. If I look at the system in VMD
> with periodic images, it seems like the outer edges of all of the quadrants
> align perfectly to make one complete bilayer with the nighboring over the
> neighboring, but the vacuums are still there.
>
> On Thu, Sep 8, 2016 at 5:42 AM, Erik Marklund <erik.marklund at kemi.uu.se>
> wrote:
>
> > 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,
> > Erik
> >
> > > 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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