[gmx-developers] Re:Re: energy calculation fails in "-rerun" mode

Berk Hess hess at cbr.su.se
Thu May 28 09:46:12 CEST 2009

Mark Abraham wrote:
> Leontyev Igor wrote:
>>>> The problem appears when I am trying to recalculate energies and dhdl
>>>> values
>>>> using "-rerun" option.
>>> There were bugfixes for -rerun between 4.0.4 and 4.0.5. Please check
>>> release notes for this sort of thing :-) I don't know if you might
>>> still
>>> have a real issue, but please update to 4.0.5 and try again.
>> The upgrade to 4.0.5 version fixed issues 2) and 3), but still the
>> average values are not printed at the end of the log-file (see the
>> issue 1).
> I think that's intended as a feature, rather than a bug, e.g.
> http://www.gromacs.org/pipermail/gmx-commit/2009-May/001656.html. I
> don't know of a good reason either way. You can get the data you want
> from g_energy on the .edr file, of course.
> Mark
The averages were incorrect.
mdrun and g_energy use a fancy way to determine exact averages and
fluctuations over all the md steps.
Since with -rerun you usually do not have all md steps, we would need to
implement extra functionality
for -rerun. But g_energy will give you the averages, so that is not
worth the effort and the risk of more
bugs because of infrequently used code.


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