HI all,
i am currently carrying out a gromacs simualtion and the simulation has been going on for over 20days because the system is heavy but i will like to know how to check the current state of the simulation so as to know if the wall time will be enough.
Kindly help with the command to check the state or completion time.
Thanks all
You can tail the log file. It lists the steps and time. Open a terminal in the directory where the mdrun ouput files are and run the following command:
tail -f .log
Replace the with the name of the log file. -f flag instructs the tail program to follow the file in realtime. You can run it without the -f flag as well.
thanks Uttam,
you mentioned directory for the output file but i do not have any output file yet. i am running the simulation on a cluster so all i have is the job ID, how do i retrieve the log file from there.
Then, you have to ssh to the node where the job is running and then cd to the temporary directory or the scratch directory. You might need to ask your computer administrator for that, because in our cluster the temporary files are not stored in /tmp rather in a custom location called /state/partition1/scr//. You might also look in to the /tmp. In the temporary job directory you shall find the log files.
Thanks Uttam,
i was able to retrieve the log file by using the arcls and arccp commands
You calculate the Root Mean Square Deviation (RMSD) of your protein backbone, you can stop when you have convergence in the RMSD to a plateau region.
Well it is better to always put -v after the mdrun so that we know when it will possibly be completed.
Here is an example!
Normal command: gmx mdrun -deffnm nvt
Adding -v: gmx mdrun -v -deffnm nvt
Bukunmi Akinwunmi
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