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YAML files written by `yank analyze --serial` are not readable

3

To reproduce: ``` >>> import yaml >>> x = yaml.load(open('reports/Harmonic_cmethingesinglehinge0_neutral-sams-rmsd.pkl', 'r')) Traceback (most recent call last): File "", line 1, in File "/home/chodera/miniconda/lib/python3.6/site-packages/yaml/__init__.py", line 72, in load return loader.get_single_data() File...

jchodera

When restoring sampler states from storage, reassign velocities to appropriate temperature

2

I'm not sure whether this fix should go in `openmmtools.mcmc` or here in YANK, but to avoid the issue where velocities are left at zero when sampler states are restored...

jchodera

Currently, compilation with the latest `cython` leads to the warning: ``` [1/1] Cythonizing ./Yank/multistate/mixing/_mix_replicas.pyx /opt/conda/conda-bld/yank_1546368811690/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/python3.7/site-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in...

jchodera

deo999

'yank status' should not require GPU

1

Right now, `yank status` appears to require a GPU platform that supports double precision to run: ``` [chodera@lilac:c-Met_hinge_binders]$ yank status --verbose --yaml neutral-sams-rmsd.yaml /home/chodera/miniconda/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate...

jchodera

Speed up YANK calculation when dealing with large numbers of multiple states

1

Hi there, I'm running YANK with many thermodynamic states (500 states) and found the calculations were really time-consuming. The default_nsteps_per_iteration is 500, default_timestep is 2.0 fs, and with 161 hours...

bingxie4

Hi everyone, There is some difference between calculating binding free energy applying a single mutation in a protein-ligand complex using Modeller and the difference in free energy resulting from run...

fabian781

have you ever think about UI interface for easy use. my meaning can we create a GUI for YANK if there will be a UI for YANK then what are...

naveenmeena584

FIRE integrator does not fully minimize this system; ASE does

5

Hi, I am helping a labmate to minimize a rather tricky dimer system that has been built out of the separate monomers by homology modelling (against PDB `3C7N`),and some manual...

jaimergp

Migrate FIRE minimizer to openmmtools

4

This is just a reminder that we should migrate the [`FireMinimizationIntegrator`](https://github.com/choderalab/yank/blob/master/Yank/fire.py) to `openmmtools` at some point.

jchodera