Homemade scripts based on protocolGromacs, for automatic md system building.
Please visit following links for more information about installation.
The working directory is 'projects/'. The script 'runme.sh' will first check PDB files in 'projects/structures', then create new directories under 'projects/projects' for each structure, and perform MD system building, minimization, NVT equilibration, NPT equilibration, and so on, as set up in 'scripts/protocolgromacs_001'.
- Refine PDB files and copy them to 'projects/structures'.
- Update parameters for GROMACS in 'scripts/protocolgromacs_001':
- 'scripts/protocolgromacs_001/runGromacs.sh'
- 'scripts/protocolgromacs_001/mdp/*.mdp'
- Change the directory to 'projects/'.
- Run the script 'runme.sh'.
- update supporting for multiple ligands
- update logging