[gmx-users] Questions about dodecahedron box

[zhenlong li]

Thanks, Tsjerk.
Exactly as what you said, it was because split of molecules over
the boundary. It runs smoothly right now as I started with a dodecahedron
box.

best,
Zhenlong

On Thu, Oct 6, 2011 at 12:24 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Zhenlong,
>
> I guess that some molecules got split over the boundaries during
> equilibration. You have to make them whole before changing the box.
> Better to start off with a rhombic dodecahedron though.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Oct 6, 2011 at 6:29 PM, zhenlong li <zxl1000 at gmail.com> wrote:
> > Dear all,
> > My system is based on Martini, needs a dodehedron box.
> > Initially, it was minimized and equilibrated with a cubic box smoothly.
> Then
> > I used the follow command to
> > translate the box in to dodehedron:
> >              editconf -f f0.gro -bt dodecahedron  -d 2 -o vesdode.gro
> > But with this change, the simulation always blows up with the message
> below.
> >
> > Since those atoms are most at the boundary of the box, I think it is
> because
> > the overlap of boundary atoms
> > with the new box type. I tried different value for -d and -box, but still
> > have the same problem.
> >
> > Can anybody give me any hint to fix this?
> >
> > Thanks a lot!
> > Zhenlong
> >
> >
> ---------------------------------------------------------------------------------------------------------------------------------
> > Making 3D domain decomposition 7 x 4 x 3
> >
> > A list of missing interactions:
> >                 Bond of  79872 missing      7
> >             G96Angle of  50688 missing      9
> >
> > Molecule type 'DPPC'
> > the first 10 missing interactions, except for exclusions:
> >             G96Angle atoms    6    7    8      global 37638 37639 37640
> >                 Bond atoms    7    8           global 37639 37640
> >             G96Angle atoms   10   11   12      global 37642 37643 37644
> >                 Bond atoms   11   12           global 37643 37644
> >
> > Molecule type 'DUPC'
> > the first 10 missing interactions, except for exclusions:
> >             G96Angle atoms   10   11   12      global 38446 38447 38448
> >                 Bond atoms   11   12           global 38447 38448
> >
> > Molecule type 'DPPC'
> > the first 10 missing interactions, except for exclusions:
> >             G96Angle atoms    3    5    6      global 43395 43397 43398
> >                 Bond atoms    5    6           global 43397 43398
> >             G96Angle atoms    5    6    7      global 43397 43398 43399
> >
> > Molecule type 'DUPC'
> > the first 10 missing interactions, except for exclusions:
> >             G96Angle atoms    6    7    8      global 45330 45331 45332
> >                 Bond atoms    7    8           global 45331 45332
> >
> > Molecule type 'DUPC'
> > the first 10 missing interactions, except for exclusions:
> >             G96Angle atoms    5    6    7      global 57173 57174 57175
> >                 Bond atoms    6    7           global 57174 57175
> >             G96Angle atoms    6    7    8      global 57174 57175 57176
> >
> > Molecule type 'DPPC'
> > the first 10 missing interactions, except for exclusions:
> >             G96Angle atoms    6    7    8      global 63822 63823 63824
> >                 Bond atoms    7    8           global 63823 63824
> >
> >
> > --
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
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