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Hi, I am trying to simulate a flat membrane surface with a different inclusions (proteins). So how can I localize the protein manually. After the simulation how can I get an idea about the percentage …
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With the current master-branch, the csv-files generated by filters contain arbitrary lines with values of 0:
```csv
...
1000 ; 11.2715 ; -0.218625 ; -0.275806 ; -0.247365 ;
1000 ; 11.2431 ; -0.…
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When setting up an OpenMM simulation in a Jupyter Notebook to use a DCDReporter to save the trajectory and then reading the recorded trajectory into VMD to visualise it, the molecule is absent from a …
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I tried to calculate an edge that does not have a perfect mapping and got two error messages. Can you please explain the meaning behind them? What exactly is the issue here?
- 0_easy_rbfe_A_complex…
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Dear Sir,
I hope this message finds you well. I am planning to study the excited state dynamics of a system in three different pH environments. For this, I was thinking of preparing the initial sam…
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Many features exist in stardis at this point which are just found in the config schema. We should make notebooks that detail the various things you can do, like add molecules to the simulation, add va…
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https://github.com/torchmd/torchmd/blob/78063fb38ec0cff366a7d42361947e62efe8112d/torchmd/wrapper.py#L4C1-L30C59
I am using TorchMD to run molecular dynamics simulations. I have a question regarding t…
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### Your name
Anna Gerosolina
### Your affiliation
Boston College
### Please provide a clear and concise description of your question or discussion topic.
I have a goal of adding new molecules, m…
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The PatchActionConvert class represents mutation of one cell type to another (e.g. a healthy tissue cell mutating into a cancer cell). Currently it is implemented by removing the current cell, making …
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Is it possible in the current implementation of anmr/enso to introduce a way to simulate spectra with arbitrary natural abundances?
As an example, let me elaborate on the formic acid molecule, whic…