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Hello,
When calculating the free energy change for a perturbation involving only dummy atoms to dummy atoms, MBAR gives exactly zero kcal/ mol, as expected, whereas TI gives positive free energies …
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This is a thread to discuss the creation of a tutorial showing how to implement free-energy perturbation using a network, e.g. generated by LOMAP, within BioSimSpace.
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> We could use some more quantitative analysis of binding free energy, like FEP (free energy perturbation). Will take a look in a few days when I have more time.
Hi, I agree. Our coll…
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Perhaps I should reopen an issue and describe it [here](https://github.com/Gallicchio-Lab/AToM-OpenMM/issues/21#issuecomment-2212364700).
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We currently allow for the set up of perturbations for molecules, either from a file with smiles in (for hydration free energies) or sdf files (with coordinates aligned to a receptor, which could be u…
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I propose that we add a new FEP (free energy perturbation) module, as `dc.fep`.
Introduction
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Free energy perturbation has become an increasingly powerful technique in modern drug di…
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Hello,
I have been using ParmEd for a while now, and I have found it extremely useful for converting files between different MD engines. However, since my research focuses on free energy perturbati…
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Dear OpenMM team,
I am looking for a package/tutorial to do protein-protein binding free energies. I have found plenty of alchemical methods for protein-ligand but none for protein-protein. Any poi…
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Hi, I recently used this package to generate some statistical data, it failed when some of the molecules' experiment values were not provided. Is there a solution to this kind of data?
Error:
```…
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```
import openmm as mm
import openmm.app as app
import openmm.unit as unit
import numpy as np
import matplotlib.pyplot as plt
syst = mm.System()
syst.addParticle(1.0 * unit.amu)
syst.addParti…