Template-MD-start

This is how I run MD simulations on Slurm. There are two directories:

• array- the files I use to set up and start 3 MD simualtions of the same starting structure
• Normal- starts one simualtion for a larger system with simulations broken into 10ns dependencies
• Normal Improved - has more changable variables and instructions for running simulations with ligands though more needs to be changed in the tleap.input file

Generally:

1. Create a directory with your starting structure
2. copy the whole directory of one of the above places
3. Make changes in tleap.input if running with ligand, or other not just protein
4. run bash setup.bash NAME
5. run sb run_system.slurm

Improvements to the array one are still in the works, but the single one is nice and I can easily change the number of nanoseconds in a section.