Hello everyone,
I am running a simulation for 500 ns but after 200 ns I get the following error:
The input requested 100000000 steps, however the checkpoint file has already
reached step 200000000. The simulation will not proceed, because either your
simulation is already complete, or your combination of input files don't
match.
I only get this error with Gromacs 2018.4 and not with newer versions. Does anyone know how to solve this issue?
The command I am using for every 100 ns is the following:
gmx_mpi mdrun -s topol.tpr -nsteps 100000000 -plumed plumed.dat -cpi state.cpt -noappend -ntomp 2
Thanks in advance :)
You've simulated longer than you're asking mdrun to run. If you've already done 200,000,000 steps, then telling it to now run for a total of 100,000,000 steps and starting from a point in the future makes no sense, so the program exits.
Justin Lemkul Thank you for your reply. I just want to continue from 200,000,000 steps and add another 100,000,000 steps. Do you have any idea on how to do that? This is the only Gromacs version that I encounted this problem on. On other versions, my system is able to reach 500 ns without any problem.
check this link: it is too simple to do.
http://www.gromacs.org/Documentation/Howtos/Extending_Simulations
Please see the link Zana Pirkhezranian provided. The mdrun -nsteps argument (which actually no longer exists) is a development tool to override the number of steps in the .tpr file and is only for testing. It signifies the *total* number of steps to run, and is not intended for extensions.
Dear @Justin Lemkul
pls see
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
Zana Pirkhezranian yes, I'm familiar with the content, having written much of it myself :) I was pointing out to the OP that there is useful information there.
I should also note, however, that the documentation on gromacs.org is outdated and no longer updated. The current link is http://manual.gromacs.org/current/user-guide/managing-simulations.html#extending-a-tpr-file (note that tpbconv no longer exists, it is gmx convert-tpr).
@Justin you're right. now convert-tpr is valid . thanks for your information.
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