TODO

[avnikonenko]

Enhancement / New features

high-priority (1)

moderate (2)

• more pytest tests

minor (3)

• show the % value of occupancy for each interaction on the image in PLIF_occupancy.html Suggestion to include features in next version release #32

Note

May not be possible to implement in StreaMD, depends on ProLIF package (PLIF_occupancy.html is generated by ProLIF module)

• option to change the font/label color and size/bold for plif.png and plif_framemap.png Suggestion to include features in next version release #32

good to have (require external expertise)

• replace commercial Gaussian to Orca/Gamess for ligand parametrization
• add support of mixed-solvent simulations
• membrane simulations support

major changes

• add support of OpenMM (+different MD engines)

in-progress

• Verbose argument. Show in the terminal the verbose information from Gromacs Suggestion to include features in next version release #32

done

• gmx_MMPBSA_ana analysis, add possibility to run decomposition analysis enhanced run_gbsa.py #31 Suggestion to include features in next version release #32
• more convenient replicas runs Replicate runs #35
• save last frame pdb after MD
• documentation
• option to change box shape and edge distance Option to change box shape and edge distance #38

not relevant

• support of multiple receptors × multiple ligands run Feature Request: Allow Reusing Pre-generated Ligand Parameters to Avoid Repeated Antechamber Runs #44

Note

Any external help and contribution would be very appreciated!