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DevelopmentSchedule
Releases are aimed for the following deadlines
- Alpha 1 -
- Alpha 2 -
- Beta 1 -
- Beta 2 -
- Production -
Developers:
- Agastya Bhati (AB)
- Fouad Husseini (FH)
- Dave Wright (DW)
- Kristof Farkas-Pall (FP)
- Stefan Zasada (SZ)
- Limited version of builder with minimal error checking (DW)
- Vanilla MD scripts produced for NAMD, OpenMM, GROMACS (FP)
Extensions to ParmEd to allow chain/segment manipulation and header reading
Initial version limited to AMBER forcefield, need to build in flexibility
For pharma applications we require ease of building as a priority
- checks for PDB correctness
- ensure PDB and topology files are compatible
- must be able to run the commands on PDBs in user specified locations (i.e. not use fixed structure as in BAC 1.0)
A user friendly design giving users feedback on their machine is key to showing local users the new system is better than what we have
Need to ensure that we design the system to separate built systems from simulation output to allow for maximum run time flexibility
We should design in the idea of unique build/simulation IDs which will allow us to track provenance and consider more flexible storage solution later down the line
Should bear in mind need for tools to aid TIES simulations - i.e. library to get substructure matches in ligands (such as RDKit)