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
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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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