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I wanted to know if it is possible to use PyMBAR to generate a 2D Potential of Mean Force (PMF) graph using energies obtained from NAMD. The energies need to be reweighted though as I used accelerated…
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I tried the alchemical free energy calculation example for a Lennard Jones fluid (http://openmm.org/tutorials/alchemical-free-energy/) and it crashes with mbar having issues with having non-1 sum for …
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Below are verified steps to install the current BICePs version (2.0b0):
```
conda create -n biceps python=3.7
conda activate biceps
conda install numpy
conda install -c conda-forge mdtraj==1.9.3
…
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Perhaps it's time to consider writing some documentation for this toolkit? It might be a good strategy to write docs alongside the actual code, especially since this is a distributed development proj…
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What does the pymbar4 documentation need to look like? This includes:
* Docstrings
* What else?
* improve https://pymbar.readthedocs.io/en/master/? How?
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As suggested I move my post from Pymbar to here.
I am running pymbar 3.0 with the alchemical_analysis without problems except for the " -c " flag.
On the provided sample input data it is running fin…
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The Python module docs appear to be empty:
http://pymbar.readthedocs.org/en/latest/timeseries.html
Any idea how to fix this @kyleabeauchamp?
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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_…
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Hi everyone,
I just finished 2 sets of Gromacs simulation for my system (RNA+ligand). The first set has only ligand (20 runs). The second set has both RNA and ligand (30 runs). Each simulation is ru…
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I found that in line 544-548 of pymbar/fes.py you wrote
```
# how do we label the bins? if N-dimensional:
# bins[0] + bins[1]*bin_length[1]**1 + bins[2]*bin_length[2…