[gmx-users] Restarting crashed simmulation.

[Justin Lemkul]

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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>>>
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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

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