[gmx-users] check point file corrupted - umbrella sampling

[Poojari, Chetan]

Hi,

I am using Gromacs 4.5.3 and want to extend my umbrella sampling runs.

But i get an errror while running the "mdrun" step of extension command, saying "Start of file magic number mismatch, checkpoint file has 1993, should be 171817. The checkpoint file is corrupted or not a checkpoint file"


Below are the commands I have used to run the umbrella sampling run


grompp   -f md_umbrella.mdp    -c npt0.gro    -t npt0.cpt    -p topol.top    -n index.ndx    -o umbrella0.tpr


mdrun    -pf pullf-umbrella0.xvg    -px pullx-umbrella0.xvg    -s umbrella0.tpr    -o 0.cpt    -c 0.gro    -x 0.xtc


I used the below commands for extension:


tpbconv  -s  umbrella0.tpr   -extend 20000   -o umbrella_new.tpr

mdrun   -s umbrella_new.tpr   -cpi 0.cpt   -pf pullf-umbrella_new.xvg   -px pullx-umbrella_new.xvg   -o new.cpt   -c new.gro    -x new.xtc   (at this step i get the error)


I have not touched the cpt files.  Its the same as it was outputed.


Please can I know what might have gone wrong.



Kind Regards,
chetan



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