Comments (4)
Can you clarify slightly? Specifically, usually we only freeze waters that are not near where the ligand would end up, since having a ligand overlap with a frozen water would be very bad. Does that answer your question, or are you asking something different?
from blues.
I was speaking about a case in which the binding site is exposed that may allow the unfrozen water molecules (the ones which are inside the binding site) to move outside and overlap with frozen water molecules. Sorry I mentioned the ligand incorrectly.
from blues.
So, the unfrozen and frozen waters are all still physically present and fully interacting, so it's impossible that they would leave and overlap with frozen waters (the sterics would prevent that, or more specifically, they would result in moves that caused this to happen being rejected). Does that answer your question?
The final result of a move proposal (which is evaluated for acceptance or rejection) is a fully interacting system with the ligand and possibly its environment moved around. The move is accepted or rejected based on the work done in the process of (perturbation & propagation, aka relaxation) so if the final PHYSICAL configuration (with full interactions) is quite unfavorable (as it would be if there are clashes between water molecules) it will get rejected.
from blues.
Yes that absolutely answers my question. Thank you very much for that clear answer.
from blues.
Related Issues (20)
- oeommtools installation HOT 2
- Water translation & rotation HOT 2
- May ultimately need different handling of long range charge interactions HOT 2
- Tests fail with openmmtools=0.15.0 HOT 2
- Update conda packages HOT 1
- Multiple alchemical regions HOT 7
- Additions to YAML configuration file
- Update devdocs and package building instructions
- Installing from source via `setup.py` does not install required packages
- Give option for Logger to stream OR write to file. HOT 1
- TypeError with LoadParm Using "structure.restart" Property HOT 1
- Improve code readability and maintainability HOT 1
- Potential bug in syncing NCMC and MD simulation HOT 1
- Failing to deploy to anaconda cloud HOT 1
- Exception: Error compiling program when running system HOT 2
- Python compatibility issue with conda build HOT 7
- Can BLUES perform multiple ligands rotate and move HOT 2
- protocol work turned nan after RandomLigandRotationMove HOT 3
- Acceptance Ratio: 0.0 HOT 4
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from blues.