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MobleyLab
Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling
I have tested the t4-toluene example and it worked well. But when I use my own [system](https://github.com/MobleyLab/blues/files/8638294/run_NCMC.zip) , it hasn't work quite well. In this system, the ligand is greatly...
Hello, I have a system contains three ligands and I wanto to rotate and move all of them. When I use BLUES to perform such action, it raised an error...
## Description Significant changes to the overall BLUES API, where much of the refactoring is to follow similar structure to the `openmmtools` toolkit. "Move" classes are now what carry out...
## Description Updates to the side chain move class that facilitate identification of dihedral atom indices (without manual entry) as well as target rotamer bins (based on an input rotpref.yaml...
## Description Have rotatable bond moves available in the latest BLUES code ## Todos Notable points that this PR has either accomplished or will accomplish. - Test on reference system...
Dear all, I am trying to run an MCMD simulation using BLUES. When installing using Conda, I had problems setting the Cuda platform, so I am using a manually compiled...
This PR aims to incorporate internal coordinate darting moves with the existing set of moves in `BLUES`. Things that still need to be done: 1. [x] Improve docstrings 2. [x]...
This PR adds in an analysis module I've been working on that automatically identify metastable ligand binding modes using tools from PyEMMA. Included is a juypter notebook that provides a...
## Description Adds a `propRegion` option to the integrator to allow focusing the additional propagation steps either in the sterics (in the middle) or the electrostatics (at either ends of...
This PR allows the Move class the option to directly impact the acceptance ratio of a move by the `Move.acceptance_ratio` attribute. This can potentially come into effect in a variety...