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We currently have parsing functions for result from APoc. But, a dask workflow has been implemented to run TMalign directly without the wrapping of APoc. Results gathered from TMalign are formatted di…
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I am trying to perform a conformer search on octane. The resulting energy differences between some conformers are very small (see below) and visual inspection shows that these conformers are the same.…
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Hi, I have an issue with installing Atomium, blender is version 3.2.2. and Molecular nodes is 0.12.2 (I think this is the latest for Blender 3.2.X).
I tried a few times but always failed.
Also I tri…
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I'm currently having strange behavior with crest 2.12. With other jobs, the software ends its routine correctly, but with a single file, it throws a segmentation error.
```
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# Gromacs模拟结果分析
当完成50ns 的分子动力学分析后,我们要对动力学结果进行解析分析,现提供一些常用的命令分享给大家。
1. 周期性边界处理,保持分子完整性
gmx trjconv -s md.tpr -f md.xtc -o mdnoPBC.xtc -pbc mol -center
#选1(protein)和0(system)
2. .消除平动和转动
gmx trjconv -s…
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# Gromacs模拟结果分析
当完成50ns 的分子动力学分析后,我们要对动力学结果进行解析分析,现提供一些常用的命令分享给大家。
1. 周期性边界处理,保持分子完整性
gmx trjconv -s md.tpr -f md.xtc -o mdnoPBC.xtc -pbc mol -center
#选1(protein)和0(system)
2. .消除平动和转动
gmx trjconv -s…
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### Describe your issue.
The description of RMSD [here](https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.transform.Rotation.align_vectors.html) is not matched by the code implemen…
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There is no unit test associated with this operator (https://github.com/tercen/RMSD_operator). If you would like this operator to be part of the App Library, it must include [continuous integration wo…
agouy updated
2 years ago
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It works as follows
```
from pwem.emlib.image import ImageHandler
volume_data = ImageHandler().read(volume_filename).getData()
```
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The tutorial of the matter is:
https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/analysis-md-simulations/tutorial.html
The steps involving RMSD, RMSF…