yank

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We should migrate the [thermodynamic trailblazing code](https://github.com/choderalab/yank/blob/master/Yank/pipeline.py#L2282-L2648) to [openmmtools](http://github.com/choderalab/openmmtools), along with the relevant tests of this functionality. We could use this for relative and absolute free energy calculations. cc @dominicrufa

jchodera

NetCDF: HDF error

2

When I run "yank_analyze", I got the following error message: OSError: [Errno -101] NetCDF: HDF error: b'OUTPUT/experiments/solvent.nc' What is the origin of this error and how can I resolve this...

jslim-furame

@mikemhenry : If you can help us update the CI for the yank repo at some point, that would be fantastic.

jchodera

Fix/support python 310

4

In python 3.10, Mapping and MutableMapping live in collections.abc and not collections. This supports importing Mapping and MutableMapping from python 3.10 and < python 3.10 We can either add this...

mikemhenry

generate_free_energy() fails because standard state correction is missing from the reporter

1

When running the `yank analyze report` command one an openmmtools generated repex trajectory, I am getting the following error: ```Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. Rendering notebook as...

zhang-ivy

extend on resume

1

This PR allows the number of timesteps to be increased upon resuming a simulation. See https://github.com/choderalab/openmmtools/pull/604

jfennick

Cannot apply the restraint. No receptor-ligand complex could be found.

1

Hello, I have just started using Yank to do the prediction of absolute free energy. The tutorial for T4 lysosome with a small probe went smoothly however since I am...

JacekKedzierski

Hi, I am new to study YANK for the calculation of NaTFSI solvation free energy in 1,2-Dimethoxyethane (DME). So, I designed the system using `.gro` file and `.top` file. Here...

Dropletsimuli

difference in experimental and calculated binding free energy for p-xylene -T4Lysozyme example

6

I tried the example of absolute binding energy calculation of p-Xylene to T4-Lysozyme in explicit solvent with the yaml file provided in the website withot any changes. My results show...

vemaparna

Is it possible to use enhanced sampling algorithms such as REST/REST2?

1

In commercial software such as Schrödinger's FEP+, FEP is accelerated by enhanced sampling methods such as REST2, is it possible to achieve a similar function in yank? In the help...

jackzzs