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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…
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We should consider adding classes to load Tinker files. This is related to #4661, which is about converting Tinker files to OpenMM force fields, but it would be even better to be able to load the fil…
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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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Hi, I have a PDB file of my protein-ligand complex. I would like to do the following, and I'm wondering if it's easily achievable using OpenMM.
First, I would like to create a script and perform an…
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Hello,
I'm trying to parameterize a fluorescent ligand in a protein using Espaloma template generator but I'm struggling to understand how to fix such an issue. It does not look self-explanatory an…
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GROMACS version: 2024.2
GROMACS modification: No
Hello, I'm currently analyzing a few molecules to cross 1,2-Dioleoyl-sn-Glycero-3-Phosphocholine
(DOPC) bilayer. I tried creating DOPC bilayer us…
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We need a new grunt task in chipper for writing an XML file to the build directory. This file tells the website which translations exist for a sim. It should have the following form:
``` xml
…
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**Describe the bug**
Calling Force estimator from Legacy code leads to an error which was not present in the past. This is an attempt at reproducing the Paper on MDF using the input files in the MDF …
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## Expected behavior
when calculating the chemical potential of ring molecules (e.g. the cyclohexane in the example folder) as a mixture of two identical components (e.g. species 1 - 200 molecules of…