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

[Efrat Noy]

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   14.00.0

   Energies (kJ/mol)
   Bond  Angle Ryckaert-Bell.  Improper Dih.  LJ-14
1.95260e+011.32951e+021.29144e+023.99233e-014.69282e+01
 Coulomb-14LJ (SR)   Coulomb (SR)  Potential Pressure (bar)
   -3.24612e+03   -3.33371e+014.24793e+031.29742e+030.0e+00


Second minimization:
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
   Bond  Angle Ryckaert-Bell.  Improper Dih.  LJ-14
2.24603e+011.31903e+021.29221e+023.98797e-014.61009e+01
 Coulomb-14LJ (SR)   Coulomb (SR)  Potential Pressure (bar)
   -3.24585e+03   -3.32600e+014.24778e+031.29876e+030.0e+00

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

[Mark Abraham]

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   14.00.0
   Energies (kJ/mol)
   Bond  Angle Ryckaert-Bell.  Improper Dih.  
LJ-14
1.95260e+011.32951e+021.29144e+023.99233e-01
4.69282e+01
 Coulomb-14LJ (SR)   Coulomb (SR)  Potential Pressure 
(bar)
   -3.24612e+03   -3.33371e+014.24793e+031.29742e+03
0.0e+00

_/Second minimization/_:
   Step   Time Lambda
  00.00.0
   Energies (kJ/mol)
   Bond  Angle Ryckaert-Bell.  Improper Dih.  
LJ-14
2.24603e+011.31903e+021.29221e+023.98797e-01
4.61009e+01
 Coulomb-14LJ (SR)   Coulomb (SR)  Potential Pressure 
(bar)
   -3.24585e+03   -3.32600e+014.24778e+031.29876e+03
0.0e+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.


Mark
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