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

[Berk Hess]

Hi,

I was not at all questioning the usefulness of the -rerun option.
I just meant to say that a user that has figured out how to properly
first run a simulation and then use mdrun -rerun can also use g_energy
afterwards.

Personally I nearly never use the averages printed in the log file.
Grepping output is much easier from g_energy than it is from the log file.
And it is not more effort either, in one case you have to use 'more',
in the other 'g_energy'.

Berk

Mark Abraham wrote:
> 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.
>
> Mark
>
>>>> 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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