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
[email protected]
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