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In the original `openmm\Lib\site-packages\openmm\app\internal\amber_file_parser.py`, there is a function called `getNonbondTerms`. Its content is as follows (see the image below):
![original_code…
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Using the default config, and the Nvidia production drivers, the fabric manager extension keeps crashing. It exits, with an error compalining that `FABRIC_NODE_CONFIG_FILE` is invalid.
What I've t…
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## The fix for this has been Back-ported to 3.11 at https://github.com/libgeos/geos/commit/5297e1e7d87a58708c2389a4bcce3e8b4f1f57e5
## Expected behavior and actual behavior.
Calling `.simplify(tol…
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We need topology files for the following ligands:
1. CAFFEINE
2. ATP
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**Describe the bug**
Is it possible to apply the self-exclusion random walk method to polymers not built using polyply. I have a GROMACS .top input from OpenFF-interchange (attached), with associated…
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```
1210.32444691658|debug|test_tablets
1199.00373029709|debug|test_tablets_migration
```
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**Describe the bug**
I get an error message when I try to save functions to a checkpoint file.
**Steps to Reproduce**
```
from firedrake import *
mesh = IcosahedralSphereMesh(radius=1.0,
…
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**Describe the bug**
Glive view faileds to load after CNCLI system services are enabled.
**Steps to reproduce the behavior:**
1. Run through per-requesites, install and run node.
2. Upon loadin…
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It is well-known that preparing the files for molecular dynamic (MD) simulation of protein-ligand complex is a tedious process, which includes preparing ligand topology, solvation, adding ions, energ…
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**Describe the bug**
When the part described in the attached .scad file is exported to .stl, it produces a file with many errors. The errors are reported by PrusaSlicer. PS "repairs" the errors and p…