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Possible bug when attempting to run PBMETAD in namd2-cuda v2.13 patched with plumed v2.6.
Tried to run the basic PBMETAD distance calculation from the docs and system crashed with atoms moving too…
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I have generated the amber topology for a small molecule (Smiles: `C([C@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O)O`).
The system is just a small molecule running in vacuum.
This topology and coordinate run…
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IMPORTANT: This section is for code-related bugs. For usage issues, please go to the [Support Forums](https://sourceforge.net/p/dwsim/discussion/).
**Describe the bug**
There is a conversion react…
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Add the analysis of converging fraction R_c from the paper
S. Fan, B. I. Iorga, and O. Beckstein. Prediction of octanol-water partition coefficients for the SAMPL6- log P molecules using molecula…
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## 🚀 Feature
The onnx in pytorch can not export a model include a torch.autograd.grad.
## Motivation
In molecular dynamics, machine learning potential (MLP) has been a popular way to accelerate t…
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**Describe the bug**
Solvate a system with rhombic dodecahedron square box would give a non-integer degree
**To Reproduce**
```
import BioSimSpace.Sandpit.Exscientia as BSS
mol = BSS.Parameters…
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Debian Bullseye/Jupyterlab
Copied making-it-rain-main files and sub-directories to Miniconda/envs/Jupyterlab/CC. Opened CHARMM_GUI in Notebook. Here are the results:
Open In Colab
Hello the…
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### Bug summary
tleap failed when querying _GMXMMPBSA_leap.in
### Terminal output
```bash
[INFO ] Generating AMBER Compatible PDB Files...
[INFO ] Changing the Complex residues name format f…
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I'd like to propose we consider bringing in @egallicc's excellent Alchemical Transfer Method (ATM) plugin into the main OpenMM repo.
ATM has now been extensively validated for computing absolute ([…