[gmx-users] extending a simulation after it get stopped because of queue time limit

[Chandan Choudhury]

On Sat, Feb 25, 2012 at 12:09 PM, priya thiyagarajan <
priya.thiyagarajan09 at gmail.com> wrote:

> hello sir,
>
> i was performing simulation for 30ns.
> due to queue time limit my mdrun stopped at 11.6ns.. then i extended my
> simulation using these two commands
>
> *tpbconv -s md.tpr -extend 20000 -o newmd.tpr
> *



I suppose you donot need to extend as the information to execute for 30ns
is contained in the md.tpr. What you need to is to just include -cpi
state.cpt while resubmitting your job.
i.e.,

*mdrun -s md.tpr -cpi state.cpt **-o md.trr -c md.gro -e md.edr -g md.log **-x
traj.xtc*
*
*
*
*
Chandan

*
> mdrun -s newmd.tpr -o md.trr -c md.gro -e md.edr -g md.log -cpi state.cpt
> -x traj.xtc -append
> *
>
> when i submit my mdrun
> i got error as
>
>
>
> Output file appending has been requested,
> but some output files listed in the checkpoint file state.cpt
> are not present or are named differently by the current program:
> output files present: md.log md.trr md.edr
> output files not present or named differently: traj.xtc
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.5
> Source code file: checkpoint.c, line: 2146
>
> Fatal error:
> File appending requested, but only 3 of the 4 output files are present
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
>
> but i had traj.xtc file in my folder..
>
>
> then again i checked my folder and again submitted my job..
> this time i got different error..
>
> i dono why i am getting like this...
>
> i got error as
>
> Reading file newmd.tpr, VERSION 4.5.5 (single precision)
> Starting 8 threads
>
> Reading checkpoint file state.cpt generated: Fri Feb 17 19:46:58 2012
>
>
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.5
> Source code file: checkpoint.c, line: 1757
>
> Fatal error:
> Failed to lock: md.log. Function not implemented.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
>
> same command i used but i got different errors each time..
>
> can anyone please help me with your answer..
>
> i searched in users list.. but i didnt get the point..
>
> please help with your answer.
>
> thanking you,
>
>
>
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--
Chandan kumar Choudhury
NCL, Pune
INDIA
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