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

[Tsjerk Wassenaar]

Hi Lin,

> I used Gromacs version 3.3.3.

There is no domain decomposition in gromacs 3.3.3.

Furthermore, you again give no account of what you're doing in terms
of command lines and don't show the grompp output. This is pointless.

Tsjerk

> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist