On 10/04/2011 5:40 PM, mohsen ramezanpour wrote:
Dear All
I used the following commands accoring to Extending Simulation in
gromacs/Documentation/how-tos/Extending Simulation
to extend my simulation.
I entered:
tpbconv -s npt-1.tpr -extend 100 -o npt-1-extend.tpr
nohup mpirun -np 4 mdrun -s npt-1-extend.tpr -cpi npt-1.cpt
Ii run this command on a node with 4 cpu.
the result was these files:
confout.gro , state.cpt ,md.log , traj.trr ,state_prev.cpt
,ener.edr ,
#confout.gro.1# ,#confout.gro.2# ,#confout.gro.3# ,# ener.edr.1#
,#ener.edr.2# ,#md.log.1 #,#traj.trr.1# ,#traj.trr.2# ,
I extended 4 files on 4 distinct nodes!
That's not the behaviour you were looking for. You've run the same .tpr
four times, once on each CPU. This is because mdrun was not compiled
with MPI. See the installation instructions.
it is excellent,because the number of outputs was different, for
example one node produced 3 md.log and 4 confout.gro !
The main question is:
which one of the resulted outputs are the main result? on wich do I
must analyse?
They should all be equivalent, but not necessarily binary identical.
Mark
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