Related Issues (20)
- Support for .top files
- Simulation container object
- Gromacs wrapper
- Use GromacsWrapper to interface with GROMACS
- Use MDSynthesis to hold MD data
- Allow fragment align with two alignment atoms
- Add method to build exchangeable entities
- Build alchembed wrapper HOT 1
- Build combined topology files
- Use topcat to make single moltype
- Add better default configs
- Method to use alchembed on two separate .gro files
- gmx grompp renumbers residues
- declash may split polymers in two
- Alchex output .gro files in the wrong order
- Include moltype and exchanged fields in structure/topology interface
- Add methods to alchembed module to run on single file
- Figure out what to do with three clashing molecules
- Alchex fails when loading .top file HOT 2
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