[gmx-users] Extending Simulation

Mark Abraham Mark.Abraham at anu.edu.au
Sun Apr 10 09:50:04 CEST 2011

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.


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