[gmx-users] Can you please tell me the exact command? Re: Restart a stopped simulation after a power failure? : Not working in Gromacs 5.1.4

[Adarsh V. K.]

Dear Dr. Mark,

Thank you for the prompt reply. I have been struggling with the issue for
couple month time. Would you please advise me how to use  " -deffnm " flag
in commands?

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

Will the above command will successful restart a stopped simulation and
append?, If no.... could you please type the exact command I should use to
solve the issue.

Sincerely,

Adarsh V. K.
Research Scholar (PhD)
National Institute of Technology, Calicut ( NIT C )
Kerala state, India

--------------------------------------------------------------------------
On Thu, May 18, 2017 at 7:13 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Some of your commands and outputs are inconsistent. You can't get
> md_0_1.log without e.g. using -deffnm, and you'll only get md.log if you
> don't use deffnm. But if you change that when trying to do your
> continuation, mdrun won't know how to append because you haven't told it
> that the old name. Be consistent. Your whole trajectory is present in all
> your output files, but you're going to have to concatenate them yourself,
> e.g. with gmx trjcat since you didn't tell mdrun a consistent name for the
> files.
>
> GROMACS 2016 likely refuses to do your continuation, precisely so that you
> are prompted to say what you actually want, rather than mdrun trying to be
> clever and getting it wrong.
>
> Mark
>
> On Thu, May 18, 2017 at 11:03 AM Adarsh V. K. <adarsh_p130085bt at nitc.ac.in>
> wrote:
>
>> 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),
>>           # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.cpt -v
>>
>> I also tried, # gmx mdrun -s md_0_1.tpr -cpi md_0_1_prev.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.
>>
>>