Dear Dr.Mark On Sun, Apr 10, 2011 at 12:20 PM, Mark Abraham <mark.abra...@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 quantities, and all of them show a final text that means the program finished succesfully! what do you think Dr.Mark? Thanks in advance for your reply > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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