[gmx-users] Restarting crashed simmulation.

[neelam wafa]

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?

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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>
>