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yank analyze error

3

I did 10 ns GBSA simulation (number of iterations = 10000, 1 iteration = 1ps). The simulation completed successfully. However, yank analyze gives the following error pymbar.utils.ParameterError: Warning: Should have...

jslim-furame

help to do my first run!

1

Dear at Yank! I need your valuable yank software in my research project, so im committed to learn about your tool and use it properly. off course i read the...

sawstory

Questions about convergence and sampler

7

I installed the latest yank (0.25.2) and tested it using the scripts given in t4-lysozyme example directory. 1) The first question is: When I increase "default_number_of_iterations" from 500 to 2000,...

jslim-furame

[DOCS] CSS Bug with version div

1

Far from urgent, but since at some point I'll probably steal the version div from here to use in the OpenPathSampling docs, I thought I'd see if you can fix...

dwhswenson

Docs deployment is broken

1

It looks like the nightly dev build docs aren't deploying via travis: ``` Installing deploy dependencies Logging in with Access Key: ****************FVPQ /home/travis/.rvm/gems/ruby-2.4.5/gems/dpl-s3-1.10.13/lib/dpl/provider/s3.rb:71:in `chdir': No such file or directory @...

jchodera

Binding site identification?

2

Hi, possibly a very dumb question here, but I was running through the T4-lysozyme / p-xylene example, and I noticed that when I load the receptor PDB and ligand mol2...

jadeshi

Implement automatic setup of replicate calculations

1

I'm thinking of adding a `replicate` option in the YAML interface that will instruct the experiment builder to run multiple runs. It would look like something like this ```yaml experiments:...

andrrizzi

Documentation on getyank: examples missing?

4

Just installed yank with "conda install yank". Now I wonder where I can find the examples that are shown in the getyank.org/latest/quickstart.html page. I can locate the p-xylene-implicit data files...

foxth

I just realized our docs don't include the equations describing the periodic variant.

jchodera

ABFE on Thombin system problems

5

Hi there, We are trying to validate ABFE calculations by using Yank. We are interested to simulate a particular series of Thrombin inhibitors. The series is composed of weak binders...

nividic