Bash script to automate setup of multiple identical MD simulations. MD parameters are for the martini 2.2 forcefield.

1. Prepare the topology using the martinize python2.7 script (see folder martinize-script).
2. Prepare the coarse-grained protein structure file in ./gromacs/coord/
3. Run: ./chikaterasu-martini 1 [This will test if topology can be generated correctly in gromacs]
4. Run: ./chikaterasu-martini 2 [This will test if solvation worked fine]
5. Run: ./chikaterasu-martini 3 [This will test if counterions were correctly added (not yet implemented)]
6. Run: ./chikaterasu-martini 4 [This will test if a short equilibration MD trajectory can be obtained in gromacs]
7. Run: ./chikaterasu-martini 0 [This will assume everything so far went well and go to the actual production MD run]

MD parameters are adjusted by editing the gromacs .mdp files in the chika_mdp directory.

See github commits

See issues