[gmx-users] Restarting crashed simmulation.

Justin Lemkul jalemkul at vt.edu
Fri May 11 19:20:07 CEST 2018 


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
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>>>>>>>>
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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
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/Support
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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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>>>
>>

-- 
==================================================

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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