[gmx-users] Restarting crashed simmulation.

[neelam wafa]

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
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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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>
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>