On 2/11/10 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). 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.
Cheers,
Without error bars it is very hard to judge how different these are. Can
you add errorbars?
How long are the simulations at the individual data points?
Rebeca Garcia
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David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
sp...@xray.bmc.uu.se sp...@gromacs.org http://xray.bmc.uu.se/~spoel
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