Streamd

- Set default temperature to 300K
- Add Position Restraints for MCPB.py pipline
- Logo
- Prolif draw_map point_size argument
- Prolif and GBSA added directory column
- Change nvt/npt/md time and seed in user-defined mdp files only if the --seed, --nvt_time, --npt_time and --md_time arguments were explicitly set up in the StreaMD arguments list otherwise user mdp parameters will be used

- Prolif n_jobs automatic calculation
- Fixed bug with interrupted continuation runs
- Fixed bug with protein only in water simulations analysis
- Add directory information into rmsd output files for replicate runs
- Separate analysis output subdirectory
- Tests added

- Added n_jobs and protein_selection arguments to run_prolif
- Added save_traj_without_water argument to run_md

- Fixed an issue with ligand restraints during NPT and NVT
- RMSD of ligand, backbone, Active Site groups are calculated by MDanalysis and saved in 1 common output file
- Use xtc and tpr files containing no water for RMSD analysis (to prevent memory issues)
- Added additional trajectory convergence analysis (html interactive files requires plotly)
- Added plotly dependency in env.yml
- Transform xvg analysis files to csv
- Save successfully finished names of the systems to the text output file
- Calculate MMPBSA intermediate files in tmp directories for multiple run in one directory
- Add unique suffix for run_md and run_gbsa output files for simultaneous runs in the same working directory

- Added GPU support
- Use only available CPUs
- Fixed logging
- Added mdrun_per_node argument