[gmx-users] Restarting crashed simmulation.
neelam wafa
neelam.wafa at gmail.com
Fri May 11 19:28:23 CEST 2018
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
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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
>>>>
>>>> * Please search the archive at http://www.gromacs.org/Support
>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>
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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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> Gromacs Users mailing list
>
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