[gmx-users] Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

[Adarsh V. K.]

Dear gmx users,

I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a
stopped simulation after a power failure? (used 8 processor cores +
Graphics card GTX 780Ti).

I have attached the log file along with this mail.

It appeared that no details appended after restarting simulation (after
power failure at 3.5 ns), Even Though the 'terminal' Ubuntu 16.04 shows
that the simulation successfully restarted from 3.5 ns (used 8 processor
cores + Graphics card GTX 780Ti) and completed the entire 8 ns
simulation...!!. Frames...350 -> 3500 ps (not appended the log file after
the restart from 3500ps to 8000ps).

I used the command (gromacs 5.1.4),  mdrun -s md.tpr -cpi state.cpt

          # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v

I also tried, mdrun -s md.tpr -cpi state.cpt -append

------------------------------------------------------------------------------------------------
md_0_1.log : (final)
-----------------
        Step           Time         Lambda
        1765000     3530.00000        0.00000

   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    6.73096e+03    3.13198e+03    2.15931e+03    1.31375e+03    4.51549e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
    3.66659e+05   -7.80170e+03   -2.71529e+06    4.12416e+03   -2.29382e+06
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
    4.12474e+05   -1.88135e+06    3.00209e+02   -7.62778e+01    2.10104e+01
   Constr. rmsd
    2.37431e-05
-------------------------------------------------------------------------------------------------
md.log (final)
----------
        Step           Time         Lambda
        4000000     8000.00000        0.00000

Writing checkpoint, step 4000000 at Thu May 18 13:55:01 2017


   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    6.44959e+03    3.18212e+03    2.06343e+03    1.53953e+03    4.49878e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.      Potential
    3.66131e+05   -7.78489e+03   -2.71259e+06    4.78708e+03   -2.29124e+06
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure (bar)
    4.13852e+05   -1.87738e+06    3.01212e+02   -7.59495e+01    5.34060e+01
   Constr. rmsd
    2.33151e-05
---------
Force evaluation time GPU/CPU: 12.005 ms/12.263 ms = 0.979
For optimal performance this ratio should be close to 1!

               Core t (s)   Wall t (s)        (%)
       Time:   312346.797    39374.380      793.3
                         10h56:14
                 (ns/day)    (hour/ns)
Performance:        9.967        2.408
Finished mdrun on rank 0 Thu May 18 13:55:02 2017

-----------------------------------------------------------------------------------------------
But while using the command it shows only 3.5 ns of simulation. How to
solve this problem

gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur
compact

Select 0 ("System")
------------------------------------------------------------
-------------------------------------

Later I repeated the whole 8 ns simulation from beginning.... It completed
with out any issues.

Can any body tell me what happens during the power failure and why
re-starting a stopped simulation is not working.

Is it any modification in 're-start' command is required?

Regards,
Adarsh V. K.