In God We Trust Hello GMX users I am trying to run one gromacs simulation in parallel. I have successfully compiled gromacs 4 with mpi support on a cluster with x86_64 architecture with 4 cpus (intel core 2 Quad 6600). when I run mdrun with single-processor ,it works fine and everything is ok, but when I run the same simulation with 4 cpu, it finishs again normally and I don't get any error messages , but my protein breaks and box of sol becomes deformed. These are first few lines of my output (on screen) NNODES=4, MYRANK=3, HOSTNAME=localhost.localdomain NODEID=3 argc=16 NNODES=4, MYRANK=0, HOSTNAME=localhost.localdomain NNODES=4, MYRANK=2, HOSTNAME=localhost.localdomain NNODES=4, MYRANK=3, HOSTNAME=localhost.localdomain NODEID=2 argc=15 NNODES=4, MYRANK=1, HOSTNAME=localhost.localdomain NODEID=1 argc=15 NODEID=3 argc=15 NODEID=0 argc=15 here is my commands and mdp file : commands: grompp -f sp.mdp -c fprmd.gro -r fprmd.gro -p n.top -o sp.tpr -n n.ndx -maxwarn 1000 mpirun -np 4 mdrun -s sp.tpr -o sp.trr -c fsp.gro -g sp.log -e sp.edr -n n.ndx -N 4 mdf file: title = n.pdb restraining warnings = 10 cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 10000 nstcomm = 1 comm_mode = Linear comm_grps = protein nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.2 coulombtype = PME rcoulomb = 1.2 rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes emtol = 10.0 emstep = 0.01
whould you please help me to overcome this problem. Many thanks in advance for your help and your reply. Yours truly Karim Mahnam Institute of Biochemistry and Biophysics (IBB) Tehran University P.O.box 13145-1384 Tehran Iran http://www.ibb.ut.ac.ir/
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