[gmx-users] Restarting crashed simmulation.

[neelam wafa]

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.
If its not appened, will the final trajectory .xtc obtained cover the whole
simmulation or I ll have to combine both results?

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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