I'm not sure that PD has any advantage here. From memory it has to
create a 128x1x1 grid, and you can direct that with DD also.
See mdrun -h -hidden for -dd.
Mark
The contents of your .log file will be far more helpful than stdout in
diagnosing what condition led to the problem.
Mark
Dear Gromacs Enthusiasts.
I am experiencing problems with mdrun_mpi (4.5.3) on a Nehalem cluster.
Problem:
This runs fine:
mpiexec -np 72 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr
This produces a segmentation fault:
mpiexec -np 128 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr
So the only
On 23/12/2010 10:01 PM, Wojtyczka, André wrote:
Dear Gromacs Enthusiasts.
I am experiencing problems with mdrun_mpi (4.5.3) on a Nehalem cluster.
Problem:
This runs fine:
mpiexec -np 72 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr
This produces a segmentation fault:
mpiexec -np 128
Hi List,
is it possible to have the -merge option in pdb2gmx set to non-interactive?
I need to merge 8 copies of a protein into one definition (.top) because if
i don't do that all the chains are included into the .top-file. It is then not
possible for me (in an easy way) to include my
Hi, thanks for your answer!
I think this only refers to the -ff force field selection.
I tried several scripting solutions to pass y to the pdb2gmx questions
whether to do the merging or not.
Maybe my wires are just crossed but i did not find any hint to
get rid of this questions.
Can't you
Hmm...
although it is necessary to run
it through on the command line once to see what the order of arguments
should be
...exactly is the main problem as I don't know all the time how many chains
are in the files I'm processing.
Pdb2gmx asks for every chain included in your files.
Though I can
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