Dear Vitaly,
Thank you so much for your suggestion!!
I've run the simultion using one core as you suggested, and I can see two
outputs on step 0 and step 100 now ( shown on the bottom), but it still took
a while to only generate these two outputs.
Maybe it is indeed the problem of scaling as mentioned by Justin?
There are: 34001 Atoms
Charge group distribution at step 0: 1953 1973 2103 2032 2044 2072 2063 1967
Grid: 3 x 7 x 18 cells
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 1.99e-05
Initial temperature: 300.057 K
Started mdrun on node 0 Fri Aug 24 10:37:20 2012
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
6.66008e+03 3.06081e+03 7.94034e+02 2.55031e+02 8.61710e+02
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
2.40538e+03 5.11091e+04 -3.00143e+03 -4.49637e+05 -8.11103e+04
Position Rest. Potential Kinetic En. Total Energy Conserved En.
5.53187e+01 -4.68547e+05 8.57672e+04 -3.82780e+05 -3.82780e+05
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
3.00450e+02 -9.73436e+01 -2.97627e+03 3.74608e-05
DD step 4 load imb.: force 6.0%
DD step 99 load imb.: force 6.1%
Step Time Lambda
100 0.20000 0.00000
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. Improper Dih. LJ-14
1.10274e+04 2.82478e+03 1.23525e+03 2.24466e+02 1.54991e+03
Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
4.67051e+03 6.34091e+04 -3.00143e+03 -4.31792e+05 -8.19081e+04
Position Rest. Potential Kinetic En. Total Energy Conserved En.
1.44619e+04 -4.17298e+05 7.13854e+04 -3.45913e+05 -3.82303e+05
Temperature Pres. DC (bar) Pressure (bar) Constr. rmsd
2.50069e+02 -9.73436e+01 -3.79866e+02 3.45085e-06
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