[gmx-users] Restarting crashed simmulation.

Fri May 11 19:14:40 CEST 2018

On 5/11/18 1:12 PM, neelam wafa wrote:
> The previous command was :
>
> gmx mdrun -deffnm md_0_1
>
> I didn't ust -cpi falg .

Then the only explanation I can think of for what you are observing is 
that somehow md_0_1.cpt was not accessible, causing mdrun to start over 
from t = 0 and write a new set of files (because -s md_0_1.tpr does not 
write files with names md_0_1.*, only -deffnm does). Your new .log file 
should clearly indicate what time it started from. If it's t=0, then 
your loading from .cpt failed and your run started over. With new file 
names, you shouldn't have lost anything and could try to restart again 
once you identify the source of the problem.

-Justin

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

==================================================