[gmx-users] not guaranteed to be binary identical ?

[Justin A. Lemkul]

Yun Shi wrote:
> Hi all,
> 
> I am doing my MD simulations piece by piece, with -maxh and -noappend 
> options, so that I can link pieces of trajectories together afterward.
> 
> But as I did part0001 with 48 cores, and part0002 with 72 cores, the log 
> file told me that:
> 
>   #nodes mismatch,
>     current program: 72
>     checkpoint file: 48
> 
>   #PME-nodes mismatch,
>     current program: -1
>     checkpoint file: 16
> 
> Gromacs binary or parallel settings not identical to previous run.
> Continuation is exact, but is not guaranteed to be binary identical.
> 
> I do not quite understand what it really means by "binary identical"?
> 
> Would this affect my results? In other words, would using different # 
> cores for each part give me different conformational assembles from 
> using the same # cores each part?
> 

Several resources:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation
http://www.gromacs.org/Documentation/Terminology/Reproducibility

-Justin

> Thanks for any help!
> Yun
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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