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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: W…
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Eventually (3.0 release), IMHO we should move towards a clean separation of executable scripts and library calls. I think that will definitely help with code reuse and readability.
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I wanted to start a thread to discuss what additions/changes to the excellent documentation Kyle has started [http://pymbar.readthedocs.org] we might want now or in the future.
Some quick things:
- I…
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I tried to install pymbar via pip in a conda env and there seems to be some JAX problem. The way to reproduce the problem. The conda install is fine though.
Create the env
```
conda create -n tes…
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## Dependencies of BICePs
```
pymbar –> 3.0 or later
mdtraj –> 1.5.0 or later
PyYaml
matplotlib –> 2.1.2 or later
numpy –> 1.14.0 or later --------> 1.10.0 or later
```
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So one thing I've noticed is that we have lots of undocumented text files and lots of functions to read and write them.
IMHO, we should pick a set of standard formats (tab-delim or CSV) and use the P…
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I installed the latest version (0.25.2) of yank, but yank analyze does not work properly.
This is due to "multistateanalyzer.py". Look at the following lines in "multistateanalyzer.py"
(Deltaf_…
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i have done ligand simulation in water and now wantto calculate solvation free energy , i used 31 lambdas states, i got this error by using alchemical_analysis.py.
Traceback (most recent call last):
…
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The current ForceBalance code on master seems to be requiring `lxml`, `networkx`, `pymbar`, `six`, and `future` (for python 2 users) that could be added to `setup.py`. Is there a reason they are not s…
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I was having problems installing pymbar on my Mac (10.9.2). I found this information that helped me solve the problem: http://stackoverflow.com/questions/22313407/clang-error-unknown-argument-mno-fu…