A python package for large-scale simulation and analysis of molecule mixtures, espacially solvents, in openMM on high performance clusters.
Please take a look at the documentation for the installation guide and useful info.
Automated simulation setup
- covers wished parameter space for temperature, pressure and dilutions with water
- creates predefined folder structure
- packs simulation boxes (by packmol)
- stores short project description with metadata and input parameters as JSON
Simulation
- with the fast simulation engine OpenMM
- NpT to NVT to NVE ensemble according to simulation Best Practices
- semi-automated job submission to High Performance Computing Centers via SLURM
Analyses
- density
- self-diffusion-coefficients as well as finite size corrected self-diffusion-coefficient
- viscosity
- hydrogen bonds
- outputted as JSON