[gmx-users] Restarting crashed simmulation.

[Justin Lemkul]

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

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