[gmx-users] Restarting crashed simmulation.

neelam wafa neelam.wafa at gmail.com
Fri May 11 20:11:36 CEST 2018 

Hi!
does this means that i should not have used -deffnm md_0_1 in the run
command? Actually I am a student and new to gromacs and have no experties
in it.  I think I need to read more about md run command options.

Regards

On Fri, 11 May 2018 10:57 pm Mark Abraham, <mark.j.abraham at gmail.com> wrote:

> 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
> > >>>>>>>>>
> > >>>>>>>>> * 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.
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> --
> > >>>>>>>>>
> > >>>>>>>> ==================================================
> > >>>>>>
> > >>>>>> 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
> > >>>>>>
> > >>>>>> * 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.
> > >>>>>>
> > >>>>>>
> > >>>>>> --
> > >>>> ==================================================
> > >>>>
> > >>>> 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
> > >>>>
> > >>>> * 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.
> > >>>>
> > >>>>
> > >>>
> > > --
> > > ==================================================
> > >
> > > 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
> > >
> > > * 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.
> > >
> > --
> > 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.
> >
> --
> 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.
>

More information about the gromacs.org_gmx-users mailing list