[gmx-users] Extending Simulation

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Sun Apr 10 10:04:00 CEST 2011

Dear Dr.Mark

On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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.
> I think I explained bad.let me explain it more:
Suppose I entered the above commands on just one node(with 4 cpu) for
npt-1.tpr (just one time I entered these commands)

besides if you were right it would result the same outputs when I run it on
different nodes with the same commands,please see below!

>  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.
Actually I checked all of them,they are different,with different averages of
and all of them show a final text that means the program finished

what do you think Dr.Mark?
Thanks in advance for your reply

> Mark
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