[gmx-users] Restarting crashed simmulation.

Justin Lemkul jalemkul at vt.edu
Fri May 11 21:00:53 CEST 2018 


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
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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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>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>> ==================================================
>>>>>>>
>>>>>>> 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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>>>>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> 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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-- 
==================================================

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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