[gmx-users] Questions about dodecahedron box

[Tsjerk Wassenaar]

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