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I was going through the tutorial [**_Using alchemiscale to evaluate a relative binding free energy network_**](https://docs.alchemiscale.org/en/latest/tutorials/demo/Alchemiscale%20Demo.html#), and …
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When creating a workflow it can sometimes be useful to have a method for getting the lowest energy structure of a collection of jobs. For example, if we are sampling a number of coordination modes for…
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Hi @gvonsem @smoortga I thought we can keep track here of the variables we want to include in the next ntuple production. Here is a list of what I remember from our discussion. Feel free to extend it.…
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I wanted to restart the discussion about how we should best implement constant-pH methods into OpenMM, and most importantly, which layer this should be implemented into.
The best strategy is to combi…
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[Kumari, Rashmi, Rajendra Kumar, Open Source Drug Discovery Consortium, and Andrew Lynn. “G_mmpbsa —A GROMACS Tool for High-Throughput MM-PBSA Calculations.” *Journal of Chemical Information and Model…
cramg updated
3 years ago
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cramg updated
3 years ago
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We're currently introducing errors into our relative free energy calculations via dummy atoms that are coupled to multiple real atoms that do _not_ cancel between environments, as explained by this [n…
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Hi, I've been doing some tests with Perses recently which I think is a really cool tool to run repex, or neq simulations. But I saw a couple of errors when I run **neq** simulations using $python setu…
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1) specify available units and type of notation (i.e. kcal/mol vs kcal.mol-1 and kJ/mol or eV or..)
2) Everything seems crystal clear except the meaning of "(When the --relative flag is specified i…
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### Describe the bug
I am trying to fit a custom spectrum which has spectral data below 1 keV (though not usable). I am trying to fit the spectra with above 1 keV using `spec.energy_fitting_range` at…