[gmx-users] restarting the crashed run

[Mark Abraham]

No, because then the state.cpt file would be redundant :-) All you can
do re-start from the beginning, because the .tpr file only has the
initial state. You can "extend" the number of steps, but you can't
magically produce the state after the first simulation just from the
initial one. (If you can, you'll be hugely popular here, though!)

Mark

On Sun, Sep 22, 2013 at 12:03 PM, Nidhi Katyal
<nidhikatyal1989 at gmail.com> wrote:
> Thank you Justin for your reply.
> Pt 3 should be the correct way to proceed. But somehow if I have lost my
> state.cpt file, can I continue my run using following commands:
>
> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> mdrun -v -s next.tpr -o next.trr -c next.gro -g next.log -e next.ene
> -noappend
> trjcat -f previous.trr next.trr -o combine.trr
>
>
>
>
> On Sun, Sep 22, 2013 at 1:43 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 9/21/13 3:46 PM, Nidhi Katyal wrote:
>>
>>> Dear all
>>> I would like to know the difference between restarting our crashed runs by
>>> 1) first generating next.tpr using tpbconv -extend option
>>>      then running grompp with this *.tpr file
>>>
>>
>> Why would you run grompp?  If you're using it as a source of coordinates,
>> you're going to be dealing with the initial state, not the last state of
>> the previous simulation, so that's garbage.  If you're restarting a crash,
>> then presumably there is no need at all to invoke tpbconv or grompp.
>>
>>
>>       and finally running mdrun but with no cpi option
>>>
>>
>> Makes no sense.  You're basically obliterating the previous simulation.
>>
>>
>>  2) same as 1 but with -cpi option
>>>
>>
>> Still no need for grompp, but if providing -cpi to mdrun, you're resuming
>> from the correct state.
>>
>>
>>  3) using only mdrun command with cpi option and with previous *.tpr
>>>      (ie not creating new tpr by tpbconv option)
>>>
>>
>> This is the correct way to proceed.  The run will pick up from the state
>> stored in the .cpt file and proceed with the number of steps originally
>> specified in the .tpr file.
>>
>>
>>  4) using procedure 3 but with no state.cpt file
>>>
>>>
>> The run should start over.
>>
>>
>>  Secondly, if state.cpt contains all the information to continue the
>>> simulation then why the simulation should continue at all without
>>> providing
>>> these files as in procedure 1 and 4
>>>
>>>
>> Without a .cpt file, the run starts over from the beginning.
>>
>> -Justin
>>
>> --
>> ==============================**====================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
>> (410) 706-7441
>>
>> ==============================**====================
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