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I have performed a bunch of thermodynamic-integration simulations for liquid water in Gromacs, and am trying to analyze the .xvg files. I'm using Windows 10 and installed Anaconda2 (64 bit) with the g…
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Dear pymbar developers,
Is there a plan to support linux-aarch64 packages on conda-forge for pymbar (preferably
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I'm using alchemlyb as an interface to do MBAR calculations, where I found that for a set of dhdl files generated with Gromacs, mbar estimate will fail when using pymbar==3.0.5, giving:
```
Tracebac…
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If MBar is set up correctly as a python package, it should be possible to have Yank automatically install mbar when installing via pip.
I'm not sure if this is preferable to bundling mbar inside ya…
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I was trying to run the Alchemical free energy calculations example as is on a CPU and a gpu - both cases don't run to completion.
but the errors are different.
On the cpu I get
Minimizing energy…
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The statistical error is 40.48 while the bootstrap error is 0.35
The code to reproduce
```
import pymbar
import numpy as np
u_nk = np.load("u_nk.npy")
N_k = [10000] * 12
mbar = pymbar.MBA…
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Hi,
I'm analyzing free energy calculations (Gromacs-based) using alchemlyb. The analysis fails due to following error:
Warning: Should have \sum_n W_nk = 1. Actual column sum for state 0 was 0.83…
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Hi,
In the README, there should be the following line:
`>>> from pymbar import testsystems, MBAR`
instead of only
`>>> from pymbar import testsystems`
The MBAR class used in the trial p…
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I have to dump out the data I'm feeding `pymbar` to see what is causing these issues, but I'm getting some odd output from `pymbar3`:
```
/Users/choderaj/anaconda/lib/python2.7/site-packages/pymbar-3…