Bash script to automate setup of multiple identical MD simulations. MD parameters are for the martini 2.2 forcefield.
- Prepare the topology using the martinize python2.7 script (see folder martinize-script).
- Prepare the coarse-grained protein structure file in ./gromacs/coord/
- Run: ./chikaterasu-martini 1 [This will test if topology can be generated correctly in gromacs]
- Run: ./chikaterasu-martini 2 [This will test if solvation worked fine]
- Run: ./chikaterasu-martini 3 [This will test if counterions were correctly added (not yet implemented)]
- Run: ./chikaterasu-martini 4 [This will test if a short equilibration MD trajectory can be obtained in gromacs]
- 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