I am running the MD simulations for 30 ns which is 15000000 nsteps using dt= 0.02 using GROMACS software but it has terminated (after 13000000 steps) before completion due to queue limits. I would like to continue the same calculation to complete the 30ns simulation.
How should I proceed?
According to Gromacs tutorial/manual, I should use -maxh option of mdrun to continue the terminated Job.
Could anyone write me how should I use it? I am confused and not sure any more if I am extending terminated MD run. How can I specify the left number of steps and how to check total time of MD simulations?
Thank you in advance for your suggestions.
you can use the "append" option to start simulation from previous checkpoint file while over writting all other files from the point where it stopped
mdrun -s md100_ns.tpr -cpi md100_ns.cpt -deffnm md100_ns -append
Use mdrun with checkpoint file:
mdrun -s topol.tpr -cpi state.cpt
This command will continue the simulation from the point when the checkpoint file was written.
Source: http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
Dear Suniba
Thanks for replying.
I am using the same command line
gmx mdrun -s md.tpr -cpi md.cpt
but I got the errors:
Fatal error:
> File appending requested, but 1 of the 4 output files are not present or
> are named differently
> For more information and tips for troubleshooting, please check the GROMACS.
So, now What could I do?.
I also used the append option but the same problem is coming.
Look for the backup files such as #traj.xtc# and other output files
and remove the "#". then rerun the command and see if error persists
Dear Nandan Kumar,
May be you can continue your simulation as follow.
gromacs version 5:
gmx convert-tpr -f *.trr -s *.tpr -e *.edr -time 26000 -until 30000 -o new.tpr
gmx mdrun -s new.tpr
previous version:
tpbconv -f *.trr -s *.tpr -e *.edr -time 26000 -until 30000 -o new.tpr
mdrun -s new.tpr
I hope that is helpful to you and you can read the manual or use the help information for futher detail of these commands.
Yours sincerely,
Honglei
Thank You Honglei Wang for reply
Definitely, I will be use your suggestions. Before you replying, I used .tpr and .cpt of crashed production MD (mdrun) with -noappend flag and it is running fine. If I will get problems in above followd thing then definitely I will be use your suggested commands and will let you know.
you can use the "append" option to start simulation from previous checkpoint file while over writting all other files from the point where it stopped
mdrun -s md100_ns.tpr -cpi md100_ns.cpt -deffnm md100_ns -append
The MD simulation which is terminated or you want to extend can be continue by below command. The bold "md" is the name of your simulation file.
gmx mdrun -v -deffnm md -cpi md.cpt -append
If you don't have the original .trr file, (maybe you strided and delete original one because it's huge generally), you can use the following command;
gmx mdrun -deffnm Xproduction -cpi Xproduction.cpt -noappend -v
or
gmx mdrun -s Xproduction.tpr -cpi Xproduction.cpt -noappend -v
your simulation will continue from the last step you stopped. It will write new files as a new simulation but the starting steps, coordinates will be written from old information.
Follow this helpful link: http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
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