[gmx-users] Restarting crashed simmulation.
Mark Abraham
mark.j.abraham at gmail.com
Sat May 12 12:27:42 CEST 2018
Hi,
Or use the existing tool one has for a group of related files, called a
directory or folder ;-) It's not compulsory to do your whole thesis in the
same folder, too :-D
Mark
On Fri, May 11, 2018, 21:01 Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 5/11/18 2:11 PM, neelam wafa wrote:
> > 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.
>
> Use -deffnm, it saves you typing and makes your life easier, because
> instead of relying on generic, default file names, you know exactly what
> you did and what your files hold.
>
> -Justin
>
> > 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.
> >>
>
> --
> ==================================================
>
> 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.
>
More information about the gromacs.org_gmx-users
mailing list