I have no idea how to write or run a shell script, however I would like to write one that would run 288 java programs sequentially (with each outputting to a different output file.
For example, were I just to run it in bash the command I would use is:
java Grid1 < slab.gro > slab1.gro
Then the next program I would run is:
java Grid2 < slab.gro > slab2.gro
The numbers in the filenames increase sequentially up to 288, and I would like to run a shell script that will, once written, run it all for me (so I do not have to run it myself 288 times). Would I just need one line and to change the numbers on each subsequent line in the script? If that is the case, what is the line I would need? I have no experience with shell scripting, so I am unsure as how it would work.
Also, how would I run the shell script once it is written?
After that is done, I would also like to run the command:
genconf -f slab1.gro -o slab1.pdb
This would also be run 288 times, with the numbers increasing up to 288. I would run it in another shell script, as it must be done on a different server.
Any help would be really, greatly appreciated!