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

Mark Abraham Mark.Abraham at anu.edu.au
Fri May 29 07:36:14 CEST 2009

Igor Leontyev wrote:
> Well, for most of users "-rerun" might be indeed infrequently used option,
> but I have published paper based on exclusively this feature. If you 
> have an
> obtained trajectory, than it's possible to recalculate the energies with
> higher level force-field. Such an approach is legitimate if energy
> difference fluctuation between force-fields is lower than kT. There is an
> analog in quantum perturbation theory: you have an energy perturbation in
> the first order but the wave-function is perturbed only in the second order
> of the small parameter. Thus "-rerun" option provides powerful tool for
> combined force-field methods.    And, of course, the most valuable
> quantities which you can extract from simulation are average values . With
> additional effort one can be obtained by "g_energy" utility, but it's just
> preferable to have it right in the log-file. Thanks for your help.

Indeed. It seems like you might want to script g_energy to run after 
your reruns, in which case the information here 
http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive might 
be helpful.


>>> 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.
>> Berk
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