[gmx-users] Re: Continuing a simulation plus another error

Ankita naithani ankitanaithani at gmail.com
Mon Dec 24 18:43:34 CET 2012

Hi Justin,

Thank you so much for your response.

I also noticed that when I type in gmxcheck -f md.cpt to see which
version was used, I get the same fatal error of "Attempting to read a
checkpoint file of version 13 with code of version 12".

In my linux machine, the gromacs version is 4.5.5 and the one on the
cluster is also 4.5.5. I just offloaded the data from the cluster and
was trying to run the test for continuing simulation before submitting
it to the cluster for continuation.

Could you please suggest me something in this regard too. I understand
that the versions would be different but my system and cluster have
the same version of gromacs. Also, is version 13 being used  by
gromacs 4.6? In that case, how do we continue a simulation with that

If somehow someone updated the software or switched it to gromacs 4.6
in the cluster, I will then directly invoke mdrun there but I would
need to know if the command would be the same for continuing the
simulation in gromacs 4.6?


mdrun -cpi md.cpt -s md.tpr

Sorry for bothering with silly questions, my time on the cluster runs
out in 2 days so I really could do with as much help I can for now

On Mon, Dec 24, 2012 at 5:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 12/24/12 11:54 AM, Ankita naithani wrote:
>> Hi again,
>> Sorry for the repetition in email.
>> When I ran the mdrun command, I got an error of
>> "Attempting to read a checkpoint file of version 13 with code of version
>> 12"
>> Can anyone please help me with this error too?
> This means you are not using the same version of the code as the previous
> run.
>> On Mon, Dec 24, 2012 at 4:35 PM, Ankita naithani
>> <ankitanaithani at gmail.com> wrote:
>>> Hi,
>>> I am running a protein simulation for 70 ns. I had a MPI run but due
>>> to my time constraints on the server, it stopped after 28ns. Now, I
>>> want to continue the simulation from the same point  up until I use up
>>> my server time.
>>> I just wanted to confirm that there are two checkpoint files written,
>>> md.cpt and md_prev.cpt. It would be really helpful if anyone could
>>> advice as to which file would be better to choose to continue the
>>> simulation?
> Checkpoint files are written every 15 minutes by default and the names are
> recycled between (prefix).cpt and (prefix)_prev.cpt to indicate the most
> recently saved state and the previous one.  Either can be used for
> continuing the stopped run, but the current state is most advantageous to
> avoid wasted time.  The previous state is saved as a backup in case of a
> corrupted checkpoint file or frame in the trajectory that would require
> starting from a previous point.
>>> Also, I wanted a confirmation that if I use:
>>> mdrun -s topol.tpr -cpi md.cpt -append
>>> Do I also need to add -deffnm md?
> That depends entirely upon the file names present and what the original
> invocation of mdrun was.
>>> and if I run mdrun, would it then continue from say 28ns and up until
>>> the time specified in the .mdp file? The reason I wanted to confirm
>>> this is that before submitting it to the server, I ran it in my local
>>> machine and when I see the log file, it shows step 0 and Time 0.0000,
>>> does that mean it is starting the simulation from scratch because I
>>> had expected it to show me step from wherever it exited last and
>>> continue from there on.
> The run will start from scratch if for some reason the checkpoint file
> cannot be found or read for whatever reason.  If you are trying to run on a
> local machine with a different number of processors, for instance, the
> checkpoint state will not be the same so the run will start over again.
> Note that most of this information is online for quick reference:
> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#Version_4.x
> -Justin
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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Ankita Naithani

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