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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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We have found a problem in pymbar/examples/alchemical-free-energy/parsers/parser_gromacs.py with parsing large dhdl.xvg files. In slice_data(), there's a line:
f.len_first, f.len_last = (len(line.sp…
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Lee-Ping would like to be able to compute arbitrary solvation free energies for a molecule in another type of molecule.
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Following from discussion in #528 .
@jchodera proposes to add to analyze the decomposition into restraining, charging, and nonbonded free energies. This may require saving into the `nc` file the alch…
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The traces have made no sense/are not computed correctly since the SAMS refactor went in, this should be fixed
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Hey,
I was wondering how to get the lower bound/variationel free energy from the bayesian GPLVM model. Is there a way to get those values?
All the best,
Will
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Hello, I have encountered some problems when I calculate phonon free energy with dynaphopy, hope to get your help.
1. The harmonic phonon free energy calculated by dynaphopy and phonopy are very di…
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The case of **simultaneous injection and withdrawal of st-storage** objects (of type "Battery") was observed in a real-life case study. As such, I can't really provide a directly reproducible study, b…
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I find that the score is taken as the opposite number in the code. Why is the final score calculated in this way?
The equation (9) in the paper is:
![屏幕截图 2024-07-18 143313](https://github.com/user-…
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@schumannj pointed out if the initial task (i.e., `NEBWorkflow.tasks[0]`) should truly be the scf calculation or the reference image.
From the example by @u-gajera, we were considering the [0] task…