job continue

[maral afshinpour]

Dear Mario,

I ran MMPBSA for the membrane-protein system for about 1 month on the cluster and 50% of the job was completed, then my job was terminated due to the time limit, is there any way to continue it? and do you have any idea why it takes too long to complete it? please find the log file attached

Best,

Maral

[maral afshinpour]

[marioe911116]

Unfortunately, ther is now way to restart the calcualtion; BUT, I have good (?) news for you:

1- If you are running the calcualtion in a cluster, I assume you can ask for more than 1 CPU and then you could use MPI to run gmx_MMPBSA. Let's say for example you could ask for 40 cpus (and let's say 80GB of RAM), then your command line would look like this:

mpirun -np 40 gmx_MMPBSA -O -i mmpbsa.in -cs ../step7_1.tpr -ci ../ascorbic.ndx -cg 25 26 -ct ../new_nojump_trans_mol.xtc -o FINAL_RESULTS_MMPBSA.dt -eo FINAL_RESULTS_MMPBSA.csv -cp ../topol.top

2- I see you are running a decomposition analysis, at least you interested in getting the decomposition energy for all the residues, using print_res="within 4" should be more than enough

https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/examples/Decomposition_analysis/

3- I see also you are running the calcualtion over 40,000 frames... Usually 4,000 are more than enough

If you implement this suggestions, your calculation will run a lot faster and you can get the results sooner for sure