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

[chris.neale at utoronto.ca]

I am somewhat confused. When I do umbrella sampling, I use a bash  
script to set up a number of separate restrained simulations. Thus I  
would get one .cpt file for each simulation. What are you doing that  
in addition to these .cpt files you also get a state.cpt and  
state_perv.cpt? Perhaps you had better start at the beginning and  
explain what you did.

Nevertheless, if your .cpt file is indeed corrupt, then you can not  
use it. You must extract a .gro from the final frame and use it (along  
with your .trr and .edr if you like) to generate a new .tpr file that  
will start a new run from where you left off.

Chris.

-- original message --

Hello Chris,


Thank you very much for your reply. I have done following test as you  
suggested to check whether the checkpoint file are corrupted.


1) Yes, I have used  same version of gromacs for mdrun and to produce  
.cpt file.


2)  when i do gmxcheck -f  0.cpt         # i get the same error.

Fatal error:
Start of file magic number mismatch, checkpoint file has 1993, should  
be 171817
The checkpoint file is corrupted or not a checkpoint file


3)  When I do mdrun -s umbrella0.tpr       # it runs without any error.



4) My mdruns has not outputted anything like 0_prev.cpt, i just have 0.cpt.


I had run US for 24 windows, each for 10ns and produced 24 different  
cpt files. Along with these 24 different .cpt files, in the end it  
also produced state.cpt and state_prev.cpt.

When i did gmxcheck -f state.cpt    # i get

Checking file state.cpt

# Atoms  51895
Last frame         -1 time 10000.000


Item        #frames Timestep (ps)
Step             1
Time             1
Lambda           1
Coords           1
Velocities       1
Forces           0
Box              1


When i did gmxcheck -f state_prev.cpt   # i get

Checking file state_prev.cpt

# Atoms  51895
Last frame         -1 time 9730.730


Item        #frames Timestep (ps)
Step             1
Time             1
Lambda           1
Coords           1
Velocities       1
Forces           0
Box              1


I just have only one md.log file in the end, i haven't outputted  
md.log file for each window.




Kind Regards,
Chetan.


________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On  
Behalf Of Chris Neale [chris.neale at utoronto.ca]
Sent: 19 September 2011 17:59
To: gmx-users at gromacs.org
Subject: [gmx-users] check point file corrupted - umbrella sampling

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.

Chris.

-- original message --


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