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

Chris Neale chris.neale at utoronto.ca
Mon Sep 19 17:59:08 CEST 2011

I have used tpbconv -until to extend a US simulation without error, and I assume that tpbconv -extend is also fine for US simulations.

1. Are you using the same version of gromacs mdrun as you used to produce your .cpt file initially?

2. what happens when you run gmxcheck on the .cpt file?

3. what happens when you run mdrun with the umbrella0.tpr file?

4. what happens when you use 0_prev.cpt?

What I am getting at is that you have stated that the checkpoint file is corrupted in your subject line, but you have not provided any evidence of that. I do appreciate that you have pasted your exact commands. The next step is to see if there is any way to test your hypothesis that the checkpoint file is corrupted.


-- original message --


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,

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