Chih-Ying Lin wrote:
Hi
I used Gromacs version 3.3.3.
OK, but unless you need scientific continuity with earlier work, use the
much faster 4.0.7. Additionally, domain decomposition was not
implemented before 4.0, so either you're mistaken about your subject
line, or you're using a 4.0.x version of mdrun, or something.
My simulation system = one protein + 20 ligand + water molecules ( 7x 7x
7 )
What does (7x 7x 7) mean?
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 can't reconcile your description with any known behaviour of any
version of GROMACS. Can you post before and after screenshots on a
webpage please (e.g. photobucket).
The odds are excellent that a newish user is doing something wrong,
rather than there being a novel problem with an old version GROMACS,
however.
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.
Well, some of them may be OK, and some are ill-formed. This is not
evidence of a problem with GROMACS, but might be evidence of an
ill-formed workflow.
With one protein + 10 ligand + water molecules, ( 6 x 6 x 6 )
There is no problems like that.
You got lucky, or used a different procedure, or something. Without a
full description of your preparation protocol, there's nothing to be said.
Mark
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