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MobleyLab
Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling
In the context of SAMPL6 host-guest binding, Andrea Rizzi noted they had run into this issue: >Since it’s not possible in OpenMM’s custom forces to compute the reciprocal space component...
There's a conditional part of the log(accept) that checks for if the energy is nan and immediately rejects it. Going by nan logic, they shouldn't be accepted if they pop...
Hello, I am trying to make set of moves in which different regions (atom indices) should be perturbed. I am not sure how can this be handled in the current...
We've moved all of the nonequilibrium switching functionality from perses into [`NonequilibriumLangevinIntegrat`](https://github.com/choderalab/openmmtools/blob/master/openmmtools/integrators.py#L1266-L1368). All of the nonequilibrium integrators can be moved out of [`ncmc_switching.py`](https://github.com/MobleyLab/blues/blob/master/blues/ncmc_switching.py) and replaced by calls to [`openmmtools.integrators.NonequilibriumLangevinIntegrator`](https://github.com/choderalab/openmmtools/blob/master/openmmtools/integrators.py#L1266-L1368) with...
We've needed a simple test system for basic BLUES which will allow us to (with minimal simulation effort) verify that rotational moves are in fact working correctly and yielding correct...
We really need a benchmark set or suite where we have a couple of diverse systems we can use to check performance of different move proposal schemes/integrators/etc. We want to...
We're close to having sidechain NCMC moves working, thanks to @khburley , but I just realized we should also eventually make it so the same type of move (under a...
Gilson pointed out we should be able to test whether the MC is working properly by turning off all thermostatting and running constant energy MD and using the MC to...
Given the latest changes from PR #117 and PR #132 . I need to do the following: - [ ] Update the API docs and class diagrams - [x] Update...
After PR #117 some things that I'd like to be added to the YAML file are: - [ ] Configuring the move type - [ ] Loading a `parmed.Structure` embedded...