[gmx-users] Re: equilibrium stage runs for too long

[Clare]

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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