Dear gromacs user,
Today, I continue the MD twice in two directories from the same point of
the MD trajectory, for example 100ns, using the same CPU, same checkpoint file,
same serve node. To my surprise, the energy informations are different between
the two continued log ouput files, which are shown below.
continue_md_01.log:
Started mdrun on rank 0 Wed Nov 1 23:17:08 2017
Step Time Lambda
50000000 100000.00000 0.00000
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
4.67507e+02 1.47390e+03 1.44019e+03 6.93280e+01 8.29478e+01
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
4.17297e+02 9.82076e+03 1.12930e+05 -8.68735e+03 -1.15522e+06
Coul. recip. Potential Kinetic En. Total Energy Conserved En.
5.88613e+03 -1.03132e+06 1.63796e+05 -8.67527e+05 -1.90771e+05
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.82366e+02 -2.04258e+02 -7.74514e+02 2.31539e-06
DD step 50000019 load imb.: force 29.5% pme mesh/force 0.964
At step 50000020 the performance loss due to force load imbalance is 11.1 %
Step Time Lambda
50001000 100002.00000 0.00000
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
4.65447e+02 1.50124e+03 1.50444e+03 7.92082e+01 1.64421e+01
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
4.18616e+02 9.80230e+03 1.11198e+05 -8.68735e+03 -1.15433e+06
Coul. recip. Potential Kinetic En. Total Energy Conserved En.
5.95908e+03 -1.03208e+06 1.64017e+05 -8.68059e+05 -1.90761e+05
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.82747e+02 -2.04258e+02 -9.31332e+02 3.06123e-06
DD step 50001999 vol min/aver 0.880 load imb.: force 10.0% pme mesh/force
1.059
...
continue_md_02.log:
Started mdrun on rank 0 Wed Nov 1 23:39:51 2017
Step Time Lambda
50000000 100000.00000 0.00000
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
4.67507e+02 1.47390e+03 1.44019e+03 6.93280e+01 8.29478e+01
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
4.17297e+02 9.82076e+03 1.12930e+05 -8.68735e+03 -1.15522e+06
Coul. recip. Potential Kinetic En. Total Energy Conserved En.
5.88613e+03 -1.03132e+06 1.63796e+05 -8.67527e+05 -1.90771e+05
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.82366e+02 -2.04258e+02 -7.74505e+02 2.31539e-06
DD step 50000019 load imb.: force 18.3% pme mesh/force 0.950
At step 50000020 the performance loss due to force load imbalance is 6.9 %
Step Time Lambda
50001000 100002.00000 0.00000
Energies (kJ/mol)
Bond U-B Proper Dih. Improper Dih. CMAP Dih.
4.51321e+02 1.43914e+03 1.56368e+03 9.15439e+01 1.64274e+01
LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR)
4.07426e+02 9.84156e+03 1.12168e+05 -8.68735e+03 -1.15440e+06
Coul. recip. Potential Kinetic En. Total Energy Conserved En.
5.88309e+03 -1.03123e+06 1.62769e+05 -8.68456e+05 -1.90745e+05
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.80597e+02 -2.04258e+02 -8.80279e+02 2.64599e-06
DD step 50001999 vol min/aver 0.905 load imb.: force 32.7% pme mesh/force
1.034
...
It is obviously shown that the energy informations varied from 100002ps (the md
is continued from 100ns). Generally speaking, the two continued MD should be
same each other since the conditions are same.
Why are they different? Does it mean the MD can not be terminated or transfered
from one server to another because they are changeable if we want to
investigate the dynamic property?
Do anyone knows the problems?
Best regards,
Ouyang.
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