[gmx-users] about parallel run

[Mahnam]

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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