[gmx-users] identical energies in a rerun calculation

[Rebeca García Fandiño]

Hello,

I am trying to do a -rerun simulation in Gromacs 4.0.4 to calculate the interaction energy between 2 residues using the trajectory I already had from the previous simulation:

 

 /gpfs/apps/GROMACS/4.0.4/bin/mdrun -v -deffnm E_interaccion_Asp -dlb auto -rerun equilibrado3_19.xtc

 

I am having very strange results, since the calculation finishes without errors, however, when I look at the .log file I found that all the Energetic terms are just the same for all steps; you can see here a piece of the log file, they are identical for each step:

 

-----------------------------------------------------------------------

Charge group distribution at step 14000: 20243 20228 20307 20264 20218 20237 20184 20187 20125 20139 20268 20231 20251 20134 20223 20180
           Step           Time         Lambda
          14000       28.00000        0.00000

   Energies (kJ/mol)
          Angle       G96Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.
    3.06349e+05    1.40143e+04    1.04094e+05    1.39048e+05    2.14284e+04
          LJ-14     Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)
    8.86844e+04    3.07537e+05    8.73300e+05   -6.98493e+04   -1.05915e+07
   Coul. recip.      Potential    Kinetic En.   Total Energy    Temperature
   -3.83299e+06   -1.26398e+07    3.11453e+06   -9.52530e+06    4.64769e+02
 Pressure (bar)  Cons. rmsd ()
    1.71651e+04    0.00000e+00

DD  step 14999 load imb.: force  3.1%  pme mesh/force 0.777

Charge group distribution at step 15000: 20243 20228 20307 20264 20218 20237 20184 20187 20125 20139 20268 20231 20251 20134 20223 20180
           Step           Time         Lambda
          15000       30.00000        0.00000

   Energies (kJ/mol)
          Angle       G96Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.
    3.06349e+05    1.40143e+04    1.04094e+05    1.39048e+05    2.14284e+04
          LJ-14     Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)
    8.86844e+04    3.07537e+05    8.73300e+05   -6.98493e+04   -1.05915e+07
   Coul. recip.      Potential    Kinetic En.   Total Energy    Temperature
   -3.83299e+06   -1.26398e+07    3.11453e+06   -9.52530e+06    4.64769e+02
 Pressure (bar)  Cons. rmsd ()
    1.71651e+04    0.00000e+00

DD  step 15999 load imb.: force  3.3%  pme mesh/force 0.792

Charge group distribution at step 16000: 20243 20228 20307 20264 20218 20237 20184 20187 20125 20139 20268 20231 20251 20134 20223 20180
           Step           Time         Lambda

---------------------------------------------------------------------------------------------------

 

Could anyone tell me what could be wrong?

 

Thank you very much in advance for your help.

 

Best wishes,

 

Rebeca Garcia

Parc Cientific de Barcelona

regafan at hotmail.com


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