[gmx-users] mismatch between energies of sequential minimization runs

Mark Abraham Mark.Abraham at anu.edu.au
Thu Feb 17 14:44:22 CET 2011

On 17/02/2011 6:47 PM, Efrat Noy wrote:
> Hi,
> I am running 2 sequential minimizations with the same mdp file. As 
> expected the second minimization stops in step zero and the resulting 
> structures of the 2 minimization runs are identical (RMSD=0.0). But, 
> the energies of the last step of the first minimization (step 14) and 
> the zero step of the second minimization are not identical (see 
> below). What could be the reason for this mismatch?
> Thanks, Efrat
> /_First minimization_/:
>           Step           Time         Lambda
>              14       14.00000        0.00000
>    Energies (kJ/mol)
>            Bond          Angle Ryckaert-Bell.  Improper Dih.          
> LJ-14
>     1.95260e+01    1.32951e+02    1.29144e+02    3.99233e-01    
> 4.69282e+01
>      Coulomb-14        LJ (SR)   Coulomb (SR)      Potential Pressure 
> (bar)
>    -3.24612e+03   -3.33371e+01    4.24793e+03    1.29742e+03    
> 0.00000e+00
> _/Second minimization/_:
>            Step           Time         Lambda
>               0        0.00000        0.00000
>    Energies (kJ/mol)
>            Bond          Angle Ryckaert-Bell.  Improper Dih.          
> LJ-14
>     2.24603e+01    1.31903e+02    1.29221e+02    3.98797e-01    
> 4.61009e+01
>      Coulomb-14        LJ (SR)   Coulomb (SR)      Potential Pressure 
> (bar)
>    -3.24585e+03   -3.32600e+01    4.24778e+03    1.29876e+03    
> 0.00000e+00

EM does a step before testing for completion.The energy terms will 
differ at about the 10^-1 to 10^0 kJ/mol level you are observing. 
However, the underlying structural differences need not be detectable in 
(say) a .gro file with precision in picometres. I'd expect you would see 
some differences with "diff".

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