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Module not found after yank update

6

ModuleNotFoundError: No module named 'simtk.openmm.app.element'

gsabbih6

YANK analyze error

2

I am trying to run yank analyze after finishing my simulation successfully but i am facing errors. with yank analyze --store={experiments} command it says: (base) arma@UB:/media/arma/DATA/YANK_NEW_TRY/HIT1-explicit-output/experiments$ yank analyze --store=/media/arma/DATA/YANK_NEW_TRY/HIT1-explicit-output/experiments Warning:...

MehreenZaka

Dear yank users, I want to get free energy per time (ns). How can I get the free energy per time from yank calculation results? Best regards :)

Byun-jinyoung

CRITICAL: Experiment NaN !

5

Hi, When I perform the .yaml, always prompt the NaN error in the follow: ----------------------------------------------------------------------------------------------------------------- 2020-04-13 23:08:03,375: Single node: executing 2020-04-13 23:08:03,378: ******************************************************************************** 2020-04-13 23:08:03,378: Iteration 1/500 2020-04-13 23:08:03,378: ********************************************************************************...

kingljy0818

yaml.load issues

6

``` /Users/choderaj/miniconda/lib/python3.6/site-packages/yank/experiment.py:1168: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. ``` See: https://github.com/yaml/pyyaml/wiki/PyYAML-yaml.load(input)-Deprecation

jchodera

Please help, the examples are not working `(mdsim1) PS C:\Users\fzp281\Downloads\yank-examples-master\examples\binding\host-guest> yank script --yaml=repex.yaml nvcc warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35', 'sm_37' and 'sm_50' architectures are deprecated, and may be...

gsabbih6

This feature becomes more important when using the SAMS protocol, because the obtained free energy becomes dependent on the position of the alchemical ion for host-guest systems. In general, it...

evohringer

Cannot find counterions for region {}: Automatic pipeline does not recognize ion ligands/solutes

11

Hi, I am trying to calculate the hydration-free energy of calcium ions. While running YANk I got the following error. **ValueError: Cannot find counterions for region {}. The region has...

ShahbazQalandar

Hi, I have a problem in maintaining the initial ligand position. I use trailblazer to construct the alchemical path but I find that the ligand is drifted away from the...

isjoung

CRITICAL: Experiment NaN

2

Dear All I am performing binding free energy of ligand with protein. While reaching at step 1918 of 2000 I am getting a NAN error as below:- 2021-03-27 07:41:57,769: ********************************************************************************...

sadafrani6