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Recently, I read a nice paper named "Efficient Calculation of Small Molecule Binding in Metal−Organic Frameworks and Porous Organic Cages" from JPCC. I want to repeat the result of CO2@MOF-5 . When I …
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From what I understand in the MTD-entropy mode, dihedral angles are used as the geometric descriptors to get bias and seed structures throughout the run. Is there a way to specify the atoms for this m…
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Hello!
Thank you for providing such a convenient analysis tool! But I meet some problems when using singleCellHaystack.
When I run `res.pc20
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Dear Valdes,
After dynamics simulation, i conducted gmx mmpbsa .but i got errors.
i found in the trajectory file, rsmd is very huge for sometimes. but overall system is stable.
i got like this for …
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## Is your feature request related to a problem? ##
The new experimental `nucleicacids` analysis module contains the https://github.com/MDAnalysis/mdanalysis/blob/c01d82bb86b480c8b2ae87f36497e7fc0a72…
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**when I run pytest, it shows:**
(oggm_env) fuxp@fuxp-virtual-machine:~$ pytest --pyargs oggm
=========================================================================================== test sessi…
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**Describe the bug**
compute_irmsd_fast() and compute_irmsd_pdb2sql() give very different RMSD: 1.13 and 5.742, respectively.
**To Reproduce**
```
from pdb2sql.StructureSimilarity import Stru…
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Example 3 in the tutorial suggests to use `case.model(benchmark=True)` to benchmark on an existing pdb structure. I followed that example but couldn't find LRMSD anywhere in the output. It also looks …
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Hi, Yinan
Thanks for the great work and for providing your code and checkpoint for the followers to reproduce 3DLinker.
First, I follow your instruction in the README to reproduce the experiment…
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I follow all the instructions in README and cloned and evaluated it three times using the checkpoint you provided. The evaluating instruction is the same as in README. The dataset I am using is Versio…