[gmx-users] Timesteps don't match

[Oliver Schillinger]

Ok yes, I got that.
I should have made it clearer.
The minimization actually run for 100 steps and did not converge.
But that is a different issue.
My probelm is that it run for 100 steps according to the log file, but 
there are only 85 frames in the trajectory file even though nstxout was 
set to 1.
What happened to the rest?

On 08/29/2014 11:10 AM, Mark Abraham wrote:
> On Fri, Aug 29, 2014 at 10:05 AM, Oliver Schillinger <
> o.schillinger at fz-juelich.de> wrote:
>
>> Hi,
>> when I minimize a system for 100 steps with nstxout set to 1 I expect to
>> get a trajectory with 100 frames.
>>
>
> nsteps is the maximum number of steps. If mdrun decides it can't make
> further progress, it says so in the log file.
>
>
>> However, gmxcheck reports 85 frames only and prints several weird messages
>> that several timesteps don't match.
>> Why is that?
>>
>
> Dunno, but since there's no time in a minimization, it's not important.
>
> Mark
>
> Tested with gromacs 4.6.5 and 5.0, serial run as well as a parallel run on
>> 12 cores and 2 GPUs, always the same result.
>> Cheers,
>> Oliver
>>
>> --
>> Oliver Schillinger
>> PhD student
>>
>> ICS-6 - Structural Biochemistry
>> Building 5.8v, Room 3010
>> Phone:  +49 2461-61-9532
>> Mobile: +49 172 53 27 914
>>
>> Forschungszentrum Juelich GmbH
>> 52425 Juelich
>> Sitz der Gesellschaft: Juelich
>> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
>> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
>> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
>> Prof. Dr. Sebastian M. Schmidt
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-- 
Oliver Schillinger
PhD student

ICS-6 - Structural Biochemistry
Building 5.8v, Room 3010
Phone:  +49 2461-61-9532
Mobile: +49 172 53 27 914

Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt