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

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 20 14:41:18 CEST 2011 


Poojari, Chetan wrote:
> Hello Chris,
> 
> I followed the steps as mentioned in the umbrella sampling tutorial in gromacs.
> 
> After NPT equilibration step, i did the umbrella simulation runs. Below are the commands which i used:
> 
> 
> 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
> 
> 
> So, I had 24 such commands in my job submission script (one script i had all the grompp command and in other script i had mdrun command) for 24 windows, which  gave me 24 cpt files.
> 
> After the  final 24th window run, along with the output names specified by me it also outputted default gromacs file names state_prev.cpt, state.cpt, md.log, ener.edr.
> 
> Please can I know if its necessary to output even log files for these 24 windows.
> 
> Size of the  state.cpt or the other cpt files which i got during npt equilibration are 1.2 MB (these cpt files are okie when i do gmxcheck, it does not give any error), where as of 24 different cpt files, each has file size of 715MB. I had run simulations for 10ns on each window.
> 

Your command specifies "-o 0.cpt" so that's the problem.  The file 0.cpt is not 
a checkpoint, it is a trajectory.  The -o flag produces a .trr file.

-Justin

> 
> Kind Regards,
> chetan
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of chris.neale at utoronto.ca [chris.neale at utoronto.ca]
> Sent: 20 September 2011 13:37
> To: gmx-users at gromacs.org
> Subject: [gmx-users] check point file corrupted - umbrella sampling
> 
> 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
> 
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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