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Dear Prof.Fan
I am training FAPbI3 model, and while the RMSE during training stays within a normal range, I encounter an issue when performing molecular dynamics simulations. Specifically, the FA m…
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# Critical Fail
Critical Fail, negative molecule counts occur, some calculations are wrong in State.next_state()
Some runs create negative molecule counts, probably at the start of a simulation.
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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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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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When performing molecular dynamics (MD) simulation with a PDB file containing Zn2+ ions, the ion representation is lost after the energy minimization step.
Zinc ion part in our input pdb file:
`HE…
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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…