Dear Amber Users,
I have a question about using parallel amber.
I managed to configure and installed serial and parallel version of amber on
my desktop which has Ubuntu 64bit operating system. And it passed almost all
of the testing, for both serial and parallel.
Now I intend to run simulation on my own polymer--- dendrimer, which has a
repeat unit. The PDB file is created using Material Studio. I followed the
steps described in the tutorial and the simulation on serial version of
sander worked just fine.
Once I tried to go parallel, it gave me tons of troubles.
When I intend to launch the simulation by "mpirun -np 2 sander.MPI -O -i
eq.in -o DenG3.out -p DenG3.prmtop -c DenG3.crd -r DenG3.rst -x DenG3.mdrcd
&"
It gives me an error saying "Must have more residues than processors". So
I looked into the prmtop file and learned it is true that there is only one
residue defined. And then I looked into the pdb file generated by material
studio, the "residue sequence number" is all set 0.
So I figured it might be the problem. Then I manually change the "residue
sequence number" grouping each repeat unit to have the same "residue
sequence number". Finally there are 61 residue. Based on my understanding,
it could ran on at least 60 processors.
However, when I intend to use "antechamber" to prepare the mol2 file, it
gives me another error saying "Warning: detected more than 10 Residue
sequence numbers:" and also "cannot run judgebontype() of antechamber.c
properly, exit".
My questions is
1) Is it true that the number of residues must be greater than the number of
processors one wanted to use? So if I want to use 120 cores, do I have to
have at least 121 residues in my simulation system?
2) If the answer to my first question is positive, why I could not prepare
mol2 file using antechamber for a system only have 61 residues?
Thank you very and any comments would be greatly appreciated.
Most of the input files are attached with this email.
Best Regards
Bin
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Received on Sun Jun 12 2011 - 14:00:03 PDT
