Comments (2)
Things to try:
- The simulation is split up into multiple parts. Investigate where the trajectory boundaries lie to see if that is a likely explanation.
- Look at the actual simulation states at the kinks to see if they coincide with any particular state changes.
- Think of potential easy cases to debug this mechanism without running a full constant-pH simulation if the bug isn't anything obvious.
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This has been resolved.
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Related Issues (20)
- Create a module for BAR analysis of calibration data
- Automated plotting module
- Add adjust-to-pH feature
- Update the documentation. HOT 1
- Add counter-ion swaps for maintaining charge neutrality HOT 4
- Clean the data repo
- Decide on simulation settings:
- Decide on rest of figures for paper HOT 1
- Could protons be used for membrane proteins? HOT 2
- Calibration plotting tweaks
- Handle syn- and anti- protons for carboxylic acids in ligands
- Abl benchmarks HOT 1
- Ions are accumulating over the course of several NCMC protocols HOT 1
- Renaming of <Protons/> ffxml block for consistency.
- Add LICENSE file
- Update the netCDF recording to support SAMS details updates HOT 1
- Ideas for increasing acceptance rates
- Don't need to pass ffxml file to constructor
- Bring documentation up to date HOT 2
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