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On 17/02/2011 6:47 PM, Efrat Noy wrote:
<blockquote cite="mid:6CA01DF9C6414027A99D64B88B775D74@ad.biu.ac.il"
type="cite">
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<div><font face="Arial" size="2">Hi,</font></div>
<div> </div>
<div><font face="Arial" size="2">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? </font></div>
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<div><font face="Arial" size="2">Thanks, Efrat</font></div>
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<div> </div>
<div><font face="Arial" size="2"><em><u>First minimization</u></em>:</font></div>
<div><font face="Arial" size="2"> Step
Time Lambda<br>
14 14.00000 0.00000</font></div>
<div> </div>
<div><font face="Arial" size="2"> Energies (kJ/mol)<br>
Bond Angle Ryckaert-Bell. Improper
Dih. LJ-14<br>
1.95260e+01 1.32951e+02 1.29144e+02
3.99233e-01 4.69282e+01<br>
Coulomb-14 LJ (SR) Coulomb (SR) Potential
Pressure (bar)<br>
-3.24612e+03 -3.33371e+01 4.24793e+03
1.29742e+03 0.00000e+00</font></div>
<div> </div>
<div> </div>
<div><font face="Arial" size="2"><u><em>Second minimization</em></u>:</font></div>
<div><font face="Arial" size="2"> Step
Time Lambda<br>
0 0.00000 0.00000</font></div>
<div> </div>
<div><font face="Arial" size="2"> Energies (kJ/mol)<br>
Bond Angle Ryckaert-Bell. Improper
Dih. LJ-14<br>
2.24603e+01 1.31903e+02 1.29221e+02
3.98797e-01 4.61009e+01<br>
Coulomb-14 LJ (SR) Coulomb (SR) Potential
Pressure (bar)<br>
-3.24585e+03 -3.32600e+01 4.24778e+03
1.29876e+03 0.00000e+00</font></div>
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</blockquote>
<br>
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".<br>
<br>
Mark<br>
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