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I'm using CoolProp to compute the excess Gibbs free energy of binary mixtures. This is defined as:
`G_{excess} = G_{real} - G_{ideal solution}`
The ideal solution free energy assumes no enthalpy…
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Hey guys,
I was recommended to post this issue here by @jchodera.
I've been trying to use openmmtools' alchemy.py code to compute solvation free energies of an ethanol molecule in water. The mai…
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It would be nice to add a few test systems here:
- two Lennard-Jones particles with and without opposite charges
- two water molecules
- an artificial binding site made of Lennard-Jones atoms
- one wa…
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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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I'm experiencing some issues when trying to generate an `FEMap` with some computed DDGs and an absolute experimental DG for the reference compound. An example notebook that shows this is in https://gi…
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Hello,
I am trying to add the Keldysh ionization rate to include plasma effects for bulk samples. I have already written the equation in Ionization.jl copying the structure of the ADK rate
https:/…
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When running this prospectively, I just use random numbers in the experimental block, but is there an easier/tidier way to get the per-node (relative)absolute free energies from a set of relative free…
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The current code is not set up to change temperature or timestep via yml file. As described in teh issue, you have to use custom MDP files for each step (equilibration, FEP). This leads to problems wi…
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**In broad terms, what are you trying to do?**
Run absolute binding free energies (ABFE) for host-guest or protein-ligand systems on a scale ranging from 100-1000 systems. This is for benchmark…
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Laying out the issues for including bootstrapping in MBAR. There's essentially thee
One relatively easy thing to do is collect bootstrap samples within __init__. This can generate a set of free en…