[gmx-users] Questions about dodecahedron box

[zhenlong li]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111006/6120397c/attachment.html>