[gmx-users] Restarting crashed simmulation.
neelam wafa
neelam.wafa at gmail.com
Sat May 12 21:11:03 CEST 2018
Thanks sir Justin and sir Mark
On Sat, 12 May 2018 3:27 pm Mark Abraham, <mark.j.abraham at gmail.com> wrote:
> 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.
> >
> --
> 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