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**Describe the bug**
It seems that I cannot run the xtb when numpy is installed at the same time.
**To Reproduce**
I create the environment with the script
```
>>> environment.yml
name: test…
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Chris Chipot reported via email that there are systematic inaccuracies encountered by @HanatoK in the computation of total forces using MTS (i.e. presumably, with `timeStepFactor` > 1). @HanatoK feel…
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Hi
I am using ProDy for the first time. I tried submitting job for PCA using ProDY plugin in VMD. In last line it shows an error (see below), but It generated three files; .dcd file, .pdb file and .…
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In `main.py` the `_cmd_receive_dd ` string is used to unpack the return values of `domain_decomposition`.
However, all the variables (`positions`, `velocities`, `indices`, etc) are local to the `main…
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Thank you Ben for posting this tutorial.
I read your ppt and it helps my understanding of bcl based ncAA rotamer preparation.
As of now, I am trying to reproduce [workshop_2022's tutorial 8](htt…
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**Describe the bug**
I want to do a geometry optimisation with the dihedral fixed to a certain value
**To Reproduce**
I have the input coordinate file
```
>>> cat input.xyz
4
H -0.…
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I have a set of indices for my protein system. The indices represent atoms, that form the tetrahedral angle. My question is how to add restrains to selected indices in OpenMM framework. As far as I k…
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Currently, the Ramachandran plotter program requires the installation of the Phenix Suite in order to generate dihedral angles of the user's given protein. This is being changed to remove the reliance…
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Hi,
So I was defining link information for backbone bonds, angles and dihedrals under the link directive as follows but this information do not show up in the molecule.itp file. Is this a bug or am …
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```python
import sys; print(sys.version)
import platform; print(platform.python_imp…