Justin A. Lemkul wrote:
milad ekramnia wrote:
Dear gromacs users I am working with gromacs 4.0 and my system is a
protein under tension solvated in water under Lincs constraint .when I
run my mdrun over n nodes by mpirun I'll get n-1 trajectory files
(also the same happen for all other output files ) which as it appears
all are identical.
as far as I know each file shall represent a separate part of the box
but when I analyze the trrs the results are identical ( e.g for
g_gyrate task ) I want to now if they are exactly the same ? if yes ,
can I prevent the rest of them from being biult up ?
my mdrun command line is : mpirun -n 4 mdrun_mpi -v -s topol.tpr
Is -n the appropriate option? Some MPI implementations are different
(-np, -N, etc), and/or you may need to supply a hostfile.
and the grommp command is: grompp_mpi -v -c minimized.gro -p
topol.top -f pull.mdp -n index.ndx
I also added --enabled-mpi to my mdrun command line but it didn't work .
If you did "--enabled-mpi" then that is incorrect, and you probably
didn't actually compile with MPI support. The proper configuration
option is "--enable-mpi" so you should check that you did not make a
typo when installing Gromacs.
And additionally, I should read better before replying. The --enable-mpi option
is not an mpirun or mdrun option. It must be invoked when configuring Gromacs.
Please be sure to read the instructions here:
http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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