[gmx-users] Gromacs test sets

[Justin A. Lemkul]

Efrat Noy wrote:
> Hi everyone,
>  
> I have just installed Gromacs (version 4.0.7), run the test sets 
> (gmxtest-4.0.4) and got few failures. I looked at the relevant 
> 'checkpot.out' and 'checkvir.out' files as suggested in previous messages.
>  
> For the 'complex' tests I got no differences in the 'checkpot.out', only 
> in the 'checkvir.out'. Some of the differences in 'checkvir.out' are 
> quite large (see below example for water).
> For the 'kernel' tests I get differences both in 'checkpot.out' and in 
> 'checkvir.out' and the differences are significant (see below example 
> for kernel020).
>  
> - Should I check any other files?
> - What should I do when the differences are significant? (I just 
> installed gromacs with no errors)
>  

The test set is largely meaningless.  Please see the first few sentences here:

http://www.gromacs.org/index.php?title=Download_%26_Installation/Test-Set

-Justin

> Thanks for your help,
> Efrat
>  
>  
> ___________________________________________________________
> complex/water/checkpot.out:
>  
> There are 31 terms in the energy files
> There are 3 terms to compare in the energy files
> Files read succesfully
> ____________________________________________________________
>  
>  
> _____________________________________________________________
> complex/water/checkvir.out:
>  
> Pressure (bar)   step  50:       46893.3,  step  50:        44899
> Vir-XX           step  50:      -6211.69,  step  50:     -6371.98
> Vir-XY           step  50:      -2423.21,  step  50:     -1880.85
> Vir-XZ           step  50:       667.327,  step  50:      381.986
> Vir-YX           step  50:      -2422.22,  step  50:     -1880.17
> Vir-YY           step  50:      -3194.86,  step  50:     -2649.86
> Vir-YZ           step  50:       -2208.7,  step  50:     -2616.43
> Vir-ZX           step  50:       667.878,  step  50:      382.404
> Vir-ZY           step  50:      -2207.77,  step  50:     -2616.81
> Vir-ZZ           step  50:      -1482.41,  step  50:     -752.677
> _____________________________________________________________
>  
>  
> _____________________________________________________________
> kernel/kernel020/checkpot.out:
>  
> LJ-14            step   0:      -63.1209,  step   0:      6.50742
> Potential        step   0:      -321.601,  step   0:     -251.972
> _____________________________________________________________
>  
>  
> _____________________________________________________________
> kernel/kernel020/checkvir.out:
>  
> LJ-14            step   0:      -63.1209,  step   0:      6.50742
> Potential        step   0:      -321.601,  step   0:     -251.972
> Kinetic En.      step   0:       15.0135,  step   0:      29.0739
> Total Energy     step   0:      -306.588,  step   0:     -222.898
> Temperature      step   0:       1.93226,  step   0:      3.74185
> Pressure (bar)   step   0:      -3095.37,  step   0:     -2497.79
> Vir-XX           step   0:       1127.45,  step   0:      1075.85
> Vir-XY           step   0:        63.524,  step   0:      21.7761
> Vir-XZ           step   0:      -264.813,  step   0:     -260.354
> Vir-YX           step   0:       63.5241,  step   0:       21.777
> Vir-YY           step   0:       803.252,  step   0:      581.702
> Vir-ZX           step   0:      -264.813,  step   0:     -260.354
> Vir-ZZ           step   0:       321.207,  step   0:      176.573
> ______________________________________________________________
> 

-- 
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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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