[gmx-developers] Simulation Break => Due to bad domain decomposition ? (MPI) => Gromacs Version 3.3.3

[Chih-Ying Lin]

Hi
I used Gromacs version 3.3.3.
My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7
)
MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64   => 16 nodes in total
After doing the energy minimization, => the potential energy is extremely
high ( say, ten to the 9th order )
I visualized the " Simulation-System-EM-solvated.gro " after the energy
minimization.
Then, I found that the Simulation Sysmtem is devided into 16 domains very
clearly and the molecules (protein, ligand, and water) break into atoms in
the boundaries.
I have checked that the 20 ligands are not overlapped each other and are not
overlapped with protein from the beginning.



More, i have created 10 alike system and each is with "one protein + 20
ligand + water molecules"
Two of them get the "minus potential energy" after energy minimization and I
can continue running the MD simulation successfully.
Others of them get the "extreme high positive potential energy" and the
system is devided into 16 domains after energy minimization and the
simulation broke afterall.



With one protein + 10 ligand + water molecules, ( 6 x 6 x 6 )
There is no problems like that.


Please give me your ideas to solve the problem.

Thank you
Lin
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