On Feb 11, 2010, at 7:40 PM, Rebeca García Fandiño wrote:
Hi,
I am doing PMF calculations using Gromacs 3.3.3, and I have found
very different results using 2 different machines. Attached you can
see that the graphics are really different for both cases (about 10
KJ/mol!!). The version of Gromacs (3.3.3) and number of processors
used (2) is the same for both calculations. The .tpr files and all
the starting files are identical for both calculations. The only
thing that changes is the machine where they were carried out.
I have checked the energy files for both cases, and they are
different, but taking into account the stochastic effect, I suppose
it is normal. There are slight differences in the energies in the
step 0 for some of the windows (but in the 5th decimal number, so
they should not be important, I suppose).
Well this might be a problem but the 5th decimal is pretty far.
Any idea of the cause of the problem? Has anyone experienced similar
problems? Any suggestion will be much appreciated.
Thanks a lot for your help, in advance.
the only thing you have left is that you have not sampled enought ... so
you have not reached convergence.
Did you try to repeat the calculation on the ame machine changing the
initial velocities ?
Cheers,
Rebeca Garcia
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