[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

Thu May 18 17:40:06 CEST 2017

Hlw

Plzz use

gmx mdrun -v -deffnm md_0_1 -cpi md_0_1.cpt

On 18 May 2017 9:01 p.m., "Adarsh V. K." <adarsh_p130085bt at nitc.ac.in>
wrote:

> 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.
> >>
> >>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>