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Hi, I felt as though the AtomsBase package had a lot of potential to be a great way for all Julia chemistry and materials science folks to outsource their structures (and simulation trajectories) visu…
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## Generate larger MLM's by, e.g., fusing two or more mindless molecules into one
### How-To?
- Adding structures into one file with some distance and application of an ellipsoid potential and M…
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**Describe the bug**
Commonly, the background of the tissue volume is defined as:
background_dictionary[Tags.MOLECULE_COMPOSITION] = TISSUE_LIBRARY.constant(1e-4, 1e-4, 0.9)
Because this function…
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Fristly thanks for the great program and easy installation process.
## **OpenMM module**
Running Openmm module to refine top models:
Here is my full
```toml
run_dir = "haddock_files"
mode = …
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### Your name
Jared Brewer
### Your affiliation
University of Minnesota
### Please provide a clear and concise description of your question or discussion topic.
Hi Folks,
I'm trying to add eth…
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## Overview
I am trying to run a simple NPT simulation with multiple ligands from a single SDF file parameterised with GAFF but I am running into `ValueError`s for multiple definitions for an atom ty…
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With the current setup in `openfe` every time a molecule gets loaded with user-set partial charges the user receives a warning `Partial charges have been provided, these will preferentially be used in…
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### **Feature Request: Create a `Tracker` Class for Monitoring Simulation Metrics**
#### **Description**
We need a flexible `Tracker` class that can be inherited by other classes to track specific…
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### **Glycolysis**
- **Accuracy**: The model correctly represents glycolysis occurring in the cytoplasm, where each glucose molecule is converted into two pyruvate molecules, yielding a net gain of…
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Dear David,
I hope this message finds you well.
I am encountering problems while generating the combinatorial pharmacophore library. I have successfully acquired the super_pharmacophore.pml file…