[gmx-users] restarting the crashed run

[Nidhi Katyal]

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
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>
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