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

[George Pantelopulos]

Hi Tsjerk,

This system is from a MARTINI simulation that was mapped using the
CHARMM-GUI MARTINI to All-Atom Converter. The structure of the system is
completely transformed upon running in GMX, even running minimization for
one step.

I'll post a few quick screencaps of the system as it was input, after one
step of minimization, and after annealing here:
https://s18.postimg.org/n0jljxow9/600000particle_splitting.png

Thank you!
George

On Thu, Sep 8, 2016 at 10:11 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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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