[gmx-users] Restarting crashed simmulation.
Mark Abraham
mark.j.abraham at gmail.com
Fri May 11 19:57:41 CEST 2018
Hi,
Behaviour has changed since 5.1 to make it harder for this happen, but if
you do not call mdrun exactly the same way, older implementations of
checkpointing would try to be helpful and sometimes actually not be
helpful. This only happens if you try to over manage mdrun. It's best to
leave it alone to append with default file names, or use -noappend with
default filenames and get the part number added automatically. But if you
want to change the filenames to have a part number you manage yourself, you
have to manage everything else too...
Mark
On Fri, May 11, 2018 at 7:28 PM neelam wafa <neelam.wafa at gmail.com> wrote:
> okay,
>
> Thanks
>
> On Fri, May 11, 2018 at 5:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 5/11/18 1:18 PM, neelam wafa wrote:
> >
> >> *This is the message of gmx check for both the trajectories. I*t means
> >> that
> >> trajectory is not continuous. Am I right?
> >>
> >
> > They are continuous (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc
> starts
> > at the same time) and can be concatenated together. It appears your run
> did
> > continue from the checkpoint file. I have no explanation for why the file
> > names are not what one would expect.
> >
> > -Justin
> >
> > *gmx check -f md_0_1.xtc*
> >>
> >> Checking file md_0_1.xtc
> >> Reading frame 0 time 0.000
> >> # Atoms 67864
> >> Precision 0.001 (nm)
> >> Reading frame 200 time 2000.000
> >>
> >>
> >> Item #frames Timestep (ps)
> >> Step 273 10
> >> Time 273 10
> >> Lambda 0
> >> Coords 273 10
> >> Velocities 0
> >> Forces 0
> >> Box 273 10
> >>
> >> * gmx check -f traj_comp.xtc*
> >>
> >>
> >> Checking file traj_comp.xtc
> >> Reading frame 0 time 2720.000
> >> # Atoms 67864
> >> Precision 0.001 (nm)
> >> Last frame 13 time 2850.000
> >>
> >>
> >> Item #frames Timestep (ps)
> >> Step 14 10
> >> Time 14 10
> >> Lambda 0
> >> Coords 14 10
> >> Velocities 0
> >> Forces 0
> >> Box 14 10
> >>
> >>
> >> On Fri, May 11, 2018 at 5:12 PM, neelam wafa <neelam.wafa at gmail.com>
> >> wrote:
> >>
> >> The previous command was :
> >>>
> >>> gmx mdrun -deffnm md_0_1
> >>>
> >>> I didn't ust -cpi falg .
> >>>
> >>> On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> >>>
> >>>
> >>>> On 5/11/18 12:52 PM, neelam wafa wrote:
> >>>>
> >>>> I used this command:
> >>>>> gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt
> >>>>>
> >>>>> But I think its not appending as new files are being generated with
> >>>>> names
> >>>>> state.cpt, state_prev.cpt and traj_comp.xtc
> >>>>> while the previous files were md_0_1.cpt, md_0_1_prev.cpt and
> >>>>> md_0_1.xtc.
> >>>>> Why has it happened ? I have checked log files but not able to infer
> a
> >>>>> proper answer.
> >>>>>
> >>>>> The file names are contained within the .cpt file, and those are what
> >>>> will be written. You haven't said what your previous command was, but
> >>>> the
> >>>> use of -deffnm makes this much easier:
> >>>>
> >>>> gmx mdrun -deffnm md_0_1 -cpi
> >>>>
> >>>> You will always get clearly named files.
> >>>>
> >>>> If its not appened, will the final trajectory .xtc obtained cover the
> >>>>
> >>>>> whole
> >>>>> simmulation or I ll have to combine both results?
> >>>>>
> >>>>> Use gmx check.
> >>>>
> >>>> -Justin
> >>>>
> >>>>
> >>>> Regards
> >>>>
> >>>>>
> >>>>> On Fri, May 11, 2018 at 2:49 PM, Justin Lemkul <jalemkul at vt.edu>
> >>>>> wrote:
> >>>>>
> >>>>>
> >>>>> On 5/11/18 10:42 AM, neelam wafa wrote:
> >>>>>>
> >>>>>> Dear Sir Justin!
> >>>>>>
> >>>>>>> I have restarted the simmulation but its producing a separate log
> >>>>>>> file
> >>>>>>> starting from the step where restarted. Is it normal response or
> >>>>>>> there
> >>>>>>> is
> >>>>>>> some problem with my restart?
> >>>>>>>
> >>>>>>> That shouldn't happen; everything should be appended unless there
> was
> >>>>>>>
> >>>>>> some
> >>>>>> problem (check the .log file itself and stdout/stderr for messages).
> >>>>>> Appending is for convenience but there is no functional requirement
> >>>>>> for
> >>>>>> it
> >>>>>> (I never append on the fly by personal preference, I just
> concatenate
> >>>>>> later).
> >>>>>>
> >>>>>> -Justin
> >>>>>>
> >>>>>>
> >>>>>> Thanks in advance.
> >>>>>>
> >>>>>> On Fri, May 11, 2018 at 12:06 PM, neelam wafa <
> neelam.wafa at gmail.com>
> >>>>>>> wrote:
> >>>>>>>
> >>>>>>> Thanks Sir Justin!
> >>>>>>>
> >>>>>>> I have continued the simmulation from the last step.
> >>>>>>>>
> >>>>>>>> Regards
> >>>>>>>>
> >>>>>>>> On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul <jalemkul at vt.edu>
> >>>>>>>> wrote:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On 5/10/18 7:08 AM, neelam wafa wrote:
> >>>>>>>>
> >>>>>>>>> Hi gmx users!
> >>>>>>>>>
> >>>>>>>>> I am running a 5ns md simmulation of a protein with 2500000
> steps.
> >>>>>>>>>> It
> >>>>>>>>>> crashed at 1360000 steps due to some power problem. Now I want
> to
> >>>>>>>>>> continue
> >>>>>>>>>> this simmulation. In the manual following command is given:
> >>>>>>>>>>
> >>>>>>>>>> mdrun -s topol.tpr -cpi state.cpt
> >>>>>>>>>>
> >>>>>>>>>> but I am confused which file is state.cpt. I have got two cpt
> >>>>>>>>>> files
> >>>>>>>>>> md_1_0.cpt and md_1_0_prev.cpt. which one is to be used?
> >>>>>>>>>>
> >>>>>>>>>> Look at the time stamps of the files and inspect their contents
> >>>>>>>>>> with
> >>>>>>>>>>
> >>>>>>>>>> gmx
> >>>>>>>>> check. You will see an obvious difference in what they contain.
> >>>>>>>>> Also
> >>>>>>>>> consult the mdrun help info, which specifically addresses your
> >>>>>>>>> question.
> >>>>>>>>>
> >>>>>>>>> Also I did not get a md_1_0.gro file/ Is is due to incomplete
> >>>>>>>>> simmulation?
> >>>>>>>>> Yes, because that file is only produced from the last step.
> >>>>>>>>>
> >>>>>>>>> Also do I need to specify -append flag or not? I am using
> version
> >>>>>>>>> 5.1.5
> >>>>>>>>> -append has been the default option for many years. Again, see
> the
> >>>>>>>>> mdrun
> >>>>>>>>> help description.
> >>>>>>>>>
> >>>>>>>>> -Justin
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>> ==================================================
> >>>>>>>>>
> >>>>>>>>> Justin A. Lemkul, Ph.D.
> >>>>>>>>> Assistant Professor
> >>>>>>>>> Virginia Tech Department of Biochemistry
> >>>>>>>>>
> >>>>>>>>> 303 Engel Hall
> >>>>>>>>> 340 West Campus Dr.
> >>>>>>>>> Blacksburg, VA 24061
> >>>>>>>>>
> >>>>>>>>> jalemkul at vt.edu | (540) 231-3129
> >>>>>>>>> http://www.thelemkullab.com
> >>>>>>>>>
> >>>>>>>>> ==================================================
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>> 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
> >>>>>>>>>
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> >>>>>>>>>
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> >>>>>>>>> or
> >>>>>>>>> send a mail to gmx-users-request at gromacs.org.
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> --
> >>>>>>>>>
> >>>>>>>> ==================================================
> >>>>>>
> >>>>>> Justin A. Lemkul, Ph.D.
> >>>>>> Assistant Professor
> >>>>>> Virginia Tech Department of Biochemistry
> >>>>>>
> >>>>>> 303 Engel Hall
> >>>>>> 340 West Campus Dr.
> >>>>>> Blacksburg, VA 24061
> >>>>>>
> >>>>>> jalemkul at vt.edu | (540) 231-3129
> >>>>>> http://www.thelemkullab.com
> >>>>>>
> >>>>>> ==================================================
> >>>>>>
> >>>>>> --
> >>>>>> Gromacs Users mailing list
> >>>>>>
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> >>>>>> /Mailing_Lists/GMX-Users_List before posting!
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> >>>>>>
> >>>>>>
> >>>>>> --
> >>>> ==================================================
> >>>>
> >>>> Justin A. Lemkul, Ph.D.
> >>>> Assistant Professor
> >>>> Virginia Tech Department of Biochemistry
> >>>>
> >>>> 303 Engel Hall
> >>>> 340 West Campus Dr.
> >>>> Blacksburg, VA 24061
> >>>>
> >>>> jalemkul at vt.edu | (540) 231-3129
> >>>> http://www.thelemkullab.com
> >>>>
> >>>> ==================================================
> >>>>
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
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> >>>> /Mailing_Lists/GMX-Users_List before posting!
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> >>>>
> >>>>
> >>>
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
> > --
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