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DevelopmentSchedule
Releases are aimed for the following deadlines
- Alpha 1 - 31st March 2017
- Alpha 2 - 15th July 2017
- Beta 1 - 31st August 2017
- Beta 2 - 15th October 2017
- Production - 31st December 2017
Developers:
- Agastya Bhati (AB)
- Fouad Husseini (FH)
- Dave Wright (DW)
- Stefan Zasada (SZ)
- Limited version of builder with minimal error checking (DW)
- GROMACS job template creation (FH)
- Specification of minimal simulation input requirements (DW & AB)
- API specification (SZ)
- API wrapper around Radical Cybertools (SZ)
- API wrapper around AWS submission (SZ)
Need to chose a library to allow manipulation of PDB data - we will review the approaches taken in sasmol, Omnia PDBfixer and HTMD. (SZ, DW & AB)
- Need to consider building complicated environments such as lipid membranes
- How will we handle PDBx/mmCIF structures
Specify a templating format to allow the creation of NAMD and GMX input files from editable protocol specifications. (DW, AB & FH)
Update FabSim scripts to handle file reorganization (AB)
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)