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Bug #2950

wrong temperature reported at end of sim with uneven number of steps

Added by Marvin Bernhardt 2 months ago. Updated 15 days ago.

Status:
Accepted
Priority:
Normal
Assignee:
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

For one of my simulations i get a temperature of 3000 K reported for the last bit of 333333 steps, where it was equilibrated around 298.15 K before.

I tried to reproduce this with 333 steps, but that did not result in a spike. Therefore I include the ener.edr file. Using gmx dump, one sees the spike is in the .edr file, so this is not a problem of gmx energy.

ener.edr (822 KB) ener.edr Marvin Bernhardt, 05/13/2019 03:06 PM
grompp.mdp (540 Bytes) grompp.mdp Marvin Bernhardt, 05/13/2019 03:06 PM
conf.gro (3.05 MB) conf.gro Marvin Bernhardt, 05/13/2019 03:06 PM
ffbonded.itp (205 KB) ffbonded.itp Marvin Bernhardt, 05/13/2019 03:07 PM
ffnonbonded.itp (61.5 KB) ffnonbonded.itp Marvin Bernhardt, 05/13/2019 03:07 PM
forcefield.itp (862 Bytes) forcefield.itp Marvin Bernhardt, 05/13/2019 03:07 PM
MET.itp (880 Bytes) MET.itp Marvin Bernhardt, 05/13/2019 03:07 PM
SOL.itp (1.09 KB) SOL.itp Marvin Bernhardt, 05/13/2019 03:07 PM
topol.top (135 Bytes) topol.top Marvin Bernhardt, 05/13/2019 03:07 PM
ener_3333steps.edr (9.67 KB) ener_3333steps.edr Paul Bauer, 07/08/2019 12:58 PM
3355.tpr (1.08 MB) 3355.tpr Paul Bauer, 07/08/2019 01:42 PM
ener_3355steps.edr (9.67 KB) ener_3355steps.edr Paul Bauer, 07/08/2019 01:43 PM
md_3355steps.log (52.1 KB) md_3355steps.log Paul Bauer, 07/08/2019 01:43 PM

History

#1 Updated by Paul Bauer 15 days ago

I just reproduced this with 3333 steps in a debug build on my machine.

#2 Updated by Paul Bauer 15 days ago

so, investigating further I found that the only thing significantly diverging between the average and final write step energies is the kinetic energy contribution

The results here are from extending the previous 3333 step run to 3355 steps to have a fast reproducer

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
    5.87965e+03    3.71328e+04    6.73000e+03    0.00000e+00    6.87208e+04
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
   -8.25315e+03   -2.94160e+05    2.65487e+03   -1.81295e+05    1.66365e+06
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
    1.48235e+06    1.48278e+06    4.63189e+03    4.11956e+04    1.81575e-06

        <======  ###############  ==>
        <====  A V E R A G E S  ====>
        <==  ###############  ======>

        Statistics over 3356 steps using 34 frames

   Energies (kJ/mol)
           Bond          Angle Ryckaert-Bell.          LJ-14     Coulomb-14
    6.11285e+03    3.70713e+04    6.90941e+03    0.00000e+00    6.86842e+04
        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
   -8.27930e+03   -2.93863e+05    2.67504e+03   -1.80689e+05    1.07054e+05
   Total Energy  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
   -7.36357e+04   -7.37932e+04    2.98057e+02   -2.11207e+01    0.00000e+00

The kinetic energy seems to be wrong by a factor of 10.

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