[gmx-users] gmx mdrun -rerun issue

[Andreas Mecklenfeld]

Dear Benson,

thanks for the offer. I've used gmx traj to generate a smaller *.trr 
file, though the occuring issue seems unaffected.
I've uploaded my files to http://ge.tt/1HNpO8s2


Kind regards,
Andreas



Am 09.10.2018 um 10:48 schrieb Benson Muite:
> Current version 2018.3 seems to have re-run feature:
>
> http://manual.gromacs.org/documentation/current/user-guide/mdrun-features.html
>
> Is your input data reasonable? Might a small version be available where
> one could try this in 2018.3 to see if the same error is obtained?
>
> Benson
>
> On 10/9/18 11:40 AM, Andreas Mecklenfeld wrote:
>> Hey,
>>
>> thanks for the quick response. Unfortunately, there isn't (at least
>> not in the short-term). Which one would be suitable though?
>>
>> Best regards,
>> Andreas
>>
>>
>>
>> Am 09.10.2018 um 10:31 schrieb Benson Muite:
>>> Hi,
>>>
>>> Is it possible to use a newer version of Gromacs?
>>>
>>> Benson
>>>
>>> On 10/9/18 11:15 AM, Andreas Mecklenfeld wrote:
>>>> Dear Gromacs users,
>>>>
>>>>
>>>> I've a question regarding the rerun option of the mdrun command in
>>>> Gromacs 2016.1. It seems as if the calculation is repeatedly performed
>>>> for the last frame (until killed by the work station). The output is
>>>>
>>>> "Last frame    1000 time 2000.000
>>>>
>>>> WARNING: Incomplete header: nr 1001 time 2000"
>>>>
>>>>
>>>> My goal is to alter the .top-file (new) and calculate energies with
>>>> previously recorded coordinates (old): "gmx grompp -f old_PROD.mdp -c
>>>> old_PROD.gro -p new_topol.top -o new_PROD.tpr"
>>>>
>>>> The mdrun looks like "gmx mdrun -rerun old_PROD.trr -deffnm new_PROD"
>>>>
>>>>
>>>> Is there a way to fix this?
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> Andreas
>>>>
>>>>

-- 
M. Sc. Andreas Mecklenfeld
Technische Universität Braunschweig
Institut für Thermodynamik
Hans-Sommer-Straße 5
38106 Braunschweig
Deutschland / Germany

Tel: +49 (0)531 391-2634
      +49 (0)531 391-65685
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