[gmx-users] Re: gromacs 4.0 parallelization

milad ekramnia m.ekramnia at ph.iut.ac.ir
Mon Nov 9 03:30:49 CET 2009

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
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 .

Milad Ekramnia
Physics Department
Isfahan University of Technology

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