[gmx-users] Restarting crashed simmulation.

[neelam wafa]

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
>
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>
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