yank

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8 processes works OK: While running mpiexec.hydra -np 8 yank script --yaml=p-xylene-implicit.yaml: bash-4.2$ free total used free shared buff/cache available Mem: 131934588 5161320 114950568 1014712 11822700 124444344 Swap: 0 0...

therealchrisneale

Hello, I find that the following command takes 4 minutes to get to the point of “execute _propagate_replica(0)” but then produces no more output while still consuming CPU resources for...

therealchrisneale

Updated docker image for YANK

11

Hello, I am wondering if there is an updated docker/singularity image for YANK. I tried to use the old one: https://hub.docker.com/r/choderalab/yank and tried building my own but in vain. There...

mmagithub

See https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files for more info. The format is really nice in that it provides a "recommended citation" so that we can point people to cite the repo via zenodo +...

mikemhenry

Update yaml loader in analyze.py

1

Related to #1152 Not sure if tests are practical; will check if they get past the conda installation stage...

lilyminium

Several issues show stacktraces that ultimately end up at this line: ``` File "/root/miniconda3/lib/python3.9/site-packages/yank/analyze.py", line 336, in __del__ for phase, analyzer in self.analyzers.items(): AttributeError: 'ExperimentAnalyzer' object has no attribute 'analyzers'...

lilyminium

yank-example-hydration-phenol-Analysis-error

1

Hi, I run example of yank, run-explicit.sh, and meet the error as follow, and my Yank Version is 0.25.2. mbar is 3.0.5.dev-Unknown, openmm is 7.6.0.dev-ad113a0. dcdplugin) Could not access file...

owenustc

Stable minimization

2

I have been experiencing some instabilities which, after much difficulty, I was able to track down to the minimizer. The observed behavior is that the minimizer will finish 'successfully', but...

jfennick

I am interested in using YANK for FEP calculation in implicit solvent, however I can't see a protocol which allows a mutation from one starting topology to different one. For...

chabi-fin

Update for new OpenMM Namespace

5

Update to support openmm >= 7.6 namespace, but also support older versions of openmm as well

mikemhenry