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".
Mark
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